In [1]:
import pandas as pd 
import numpy as np
In [2]:
pd.set_option('display.max_rows', 1000)
pd.set_option('display.max_columns', 1000)
pd.set_option('display.width', 5000)
In [3]:
bact=pd.read_excel("C:/Users/KANMANIVISHWAA/Downloads/ML_Dataset_Oct22.xlsx")
bact
Out[3]:
Pathogen Family GT Endemic Severity Severity_Scale Route Tissue Sytemic Transmissibility Aid Immune_killing Immune_survival Motility
0 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
1 Aeromonas hydrophila Aeromonadaceae 0.35 0.0 0.0 2.0 Ingestion Gastrointestinal 0.0 0.0 Help 0.0 0.0 1.0
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 0.0 0.0 3.0 Vector Bloodstream 1.0 0.0 Hinders 0.0 1.0 0.0
3 Arcobacter butzleri Arcobacteraceae 0.66 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 1.0
4 Bacillus anthracis Bacillaceae 0.50 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 1.0 0.0 0.0
5 Bacillus cereus d 0.30 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 1.0
6 Bacteroides fragilis Bacteroidaceae 0.67 0.0 1.0 1.0 NaN Gastrointestinal 1.0 0.0 Noeffect 0.0 NaN 0.0
7 Bordatella pertussis Alcaligenaceae 3.80 1.0 NaN 2.0 Inahalation Respiratory 0.0 1.0 Helps 1.0 1.0 0.0
8 Brucella abortus Brucellaceae 2.00 0.0 0.0 4.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 0.0 1.0 0.0
9 Brucella melitensis Brucellaceae 2.00 0.0 0.0 2.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 1.0 0.0
10 Brucella suis Brucellaceae 2.00 0.0 0.0 3.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 0.0 1.0 0.0
11 Campylobacter jejuni Campylobacteraceae 1.50 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 1.0
12 Clostridium perfringens Clostridiaceae 0.20 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0
13 Corynebacterium diphtheriae Corynebacteriaceae 2.00 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Helps NaN 0.0 0.0
14 Coxiella burnetii Coxiellaceae 8.00 0.0 0.0 3.0 Inahalation Respiratory 1.0 0.0 Noeffect 0.0 1.0 0.0
15 E coli EHEC Enterobacteriaceae 0.33 0.0 0.0 2.0 Ingestion Gastrointestinal 1.0 1.0 Helps 1.0 1.0 1.0
16 E coli EIEC Enterobacteriaceae 0.40 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 1.0
17 E coli EPEC Enterobacteriaceae 0.40 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0
18 E coli ETEC Enterobacteriaceae 0.33 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0
19 Haemophilus ducreyi Pasteurellaceae 1.80 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Helps 1.0 1.0 1.0
20 Helicobacter pylori Helicobacteraceae 2.40 1.0 0.0 2.0 Ingestion Gastrointestinal 0.0 NaN NaN 1.0 NaN 1.0
21 Legionella pneumophila Legionellaceae 3.30 0.0 1.0 1.0 Inahalation Respiratory 0.0 0.0 Noeffect 1.0 1.0 1.0
22 Listeria monocytogenes Listeriaceae 1.00 0.0 1.0 NaN Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 1.0 1.0
23 Mycobacterium tuberculosis Mycobacteriaceae 19.00 1.0 1.0 NaN Inahalation Respiratory 1.0 1.0 Helps 1.0 1.0 0.0
24 Neisseria gonorrhoeae Neisseriaceae 0.58 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 1.0 0.0
25 Neisseria meningitidis Neisseriaceae 0.72 1.0 1.0 1.0 Inahalation Respiratory 1.0 1.0 Noeffect 0.0 0.0 0.0
26 Orientia tsutsugamushi Rickettsiaceae 9.00 0.0 1.0 1.0 Vector Bloodstream 1.0 0.0 Noeffect 0.0 1.0 0.0
27 Plesiomonas shigelloides Enterobacteriaceae 0.43 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 NaN NaN 0.0 NaN 1.0
28 Rickettsia conorii (SFG) Rickettsiaceae 4.10 0.0 0.0 2.0 Vector Bloodstream 1.0 0.0 Noeffect NaN 1.0 0.0
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Noeffect NaN 1.0 0.0
30 Rickettsia rickettsii (SFG) Rickettsiaceae 9.00 0.0 1.0 1.0 Vector Bloodstream 1.0 0.0 Noeffect 1.0 1.0 0.0
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 1.0 1.0 1.0 Ingestion Gastrointestinal 1.0 1.0 Noeffect NaN 1.0 1.0
32 Salmonella enterica s. Typhimurium Enterobacteriaceae 0.40 1.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps NaN 1.0 1.0
33 Shigella dysenteriae Enterobacteriaceae 0.67 1.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 1.0
34 Shigella flexneri Enterobacteriaceae 0.68 1.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 0.0
35 Shigella sonnei Enterobacteriaceae 0.50 1.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 0.0
36 Staphylococcus aureus Staphylococcaceae 0.40 0.0 1.0 2.0 Ingestion Gastrointestinal 1.0 1.0 Noeffect 1.0 1.0 0.0
37 Streptococcus pneumoniae Streptococcaceae 0.50 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 0.0 0.0
38 Streptococcus pyogenes (group A) Streptococcaceae 0.40 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Noeffect 1.0 1.0 0.0
39 Treponema pallidum Spirochaetaceae 33.00 1.0 1.0 1.0 Sexual Genital 1.0 1.0 Helps 0.0 NaN 1.0
40 Vibrio cholerae Vibrionaceae 0.20 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0
41 Vibrio parahaemolyticus Vibrionaceae 0.20 0.0 0.0 2.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 1.0
42 Vibrio vulnificus Vibrionaceae 0.16 0.0 1.0 1.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 0.0 1.0
43 Yersinia enterocolitica Enterobacteriaceae 0.55 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0
44 Yersinia pestis Enterobacteriaceae 1.25 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Hinder 1.0 1.0 0.0
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0
46 Leptospira interrogans Spirochaetaceae 9.00 0.0 1.0 1.0 Direct Bloodstream 1.0 0.0 Noeffect 0.0 0.0 1.0
47 Bartonella henselae Bartonellaceae 3.00 0.0 0.0 3.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 1.0
48 Bartonella bacilliformis Bartonellaceae 24.00 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Noeffect 0.0 1.0 1.0
49 Bartonella quintana Bartonellaceae 3.00 0.0 0.0 4.0 Vector Bloodstream 1.0 1.0 Noeffect 0.0 0.0 NaN
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 1.0 0.0
51 Burkholderia pseudomallei Burkholderiaceae 1.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 1.0
52 Burkholderia mallei Burkholderiaceae 0.75 0.0 1.0 1.0 Direct Cutaneous 1.0 NaN Noeffect 0.0 1.0 0.0
53 Mycoplasma pneumoniae Mycoplasmataceae 6.00 1.0 0.0 4.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 1.0 1.0
54 Mycoplasma genitalium Mycoplasmataceae 12.00 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 0.0 1.0
55 Borrelia burgdorferi Spirochaetaceae 4.00 0.0 0.0 4.0 Vector Bloodstream 1.0 0.0 Noeffect 0.0 0.0 1.0
56 Chlamydia pneumoniae Chlamydiaceae 24.00 1.0 NaN 2.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 1.0 0.0
57 Clostridium difficile Peptostreptococcaceae 0.50 0.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0
58 Ehrlichia chaffeensis Anaplasmataceae 19.00 0.0 0.0 2.0 Vector Bloodstream 1.0 0.0 Noeffect NaN 1.0 0.0
59 Klebsiella granulomatis Enterobacteriaceae NaN 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders NaN 1.0 0.0
60 Mycobacterium leprae Mycobacteriaceae 240.00 0.0 1.0 2.0 Inahalation Respiratory 1.0 1.0 Noeffect 0.0 1.0 0.0
61 Francisella tularensis tularensis (Type A) Francisellaceae 3.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0
62 Francisella tularensis holarctica (Type B) Francisellaceae 3.00 0.0 0.0 4.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0
63 Mycobacterium bovis Mycobacteriaceae 23.00 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 1.0 0.0
64 Nocardia brasiliensis Nocardiaceae 3.00 0.0 0.0 3.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 1.0 0.0
65 Erysipelothrix rhusiopathiae Erysiopelotrichaceae NaN 0.0 0.0 2.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0
66 Mycobacterium marinum Mycobacteriaceae 24.00 0.0 0.0 3.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 1.0 0.0
67 Fusobacterium nucleatum Fusobacteriaceae 0.72 1.0 NaN NaN NaN Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 0.0
68 Haemophilus influenzae Type B Pasteurellaceae 0.50 1.0 NaN 2.0 Inahalation Respiratory 1.0 1.0 Helps 0.0 0.0 0.0
69 Pasteurella multocida Brucellaceae 48.00 0.0 0.0 2.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 0.0 0.0
70 Chlamydia psittaci Chlamydiaceae 24.00 0.0 0.0 2.0 Inahalation Respiratory 0.0 0.0 NaN 0.0 1.0 0.0
71 Clostridium tetani Clostridiaceae 0.50 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 0.0 1.0
72 Enterococcus faecalis Enterococcaceae 0.50 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0
73 Streptobacillus moniliformis Leptotrichiaceae 36.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect NaN NaN 0.0
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 0.0 0.0 3.0 Direct Cutaneous 1.0 NaN Noeffect 0.0 0.0 1.0
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 0.0 0.0 3.0 NaN NaN 1.0 0.0 Noeffect 0.0 0.0 1.0
76 Acinetobacter baumannii Moraxellaceae 0.66 0.0 0.0 3.0 Direct Cutaneous 1.0 1.0 Noeffect 0.0 0.0 0.0
In [4]:
bact = bact.drop(labels=0,axis=0)
In [5]:
bact
Out[5]:
Pathogen Family GT Endemic Severity Severity_Scale Route Tissue Sytemic Transmissibility Aid Immune_killing Immune_survival Motility
1 Aeromonas hydrophila Aeromonadaceae 0.35 0.0 0.0 2.0 Ingestion Gastrointestinal 0.0 0.0 Help 0.0 0.0 1.0
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 0.0 0.0 3.0 Vector Bloodstream 1.0 0.0 Hinders 0.0 1.0 0.0
3 Arcobacter butzleri Arcobacteraceae 0.66 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 1.0
4 Bacillus anthracis Bacillaceae 0.50 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 1.0 0.0 0.0
5 Bacillus cereus d 0.30 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 1.0
6 Bacteroides fragilis Bacteroidaceae 0.67 0.0 1.0 1.0 NaN Gastrointestinal 1.0 0.0 Noeffect 0.0 NaN 0.0
7 Bordatella pertussis Alcaligenaceae 3.80 1.0 NaN 2.0 Inahalation Respiratory 0.0 1.0 Helps 1.0 1.0 0.0
8 Brucella abortus Brucellaceae 2.00 0.0 0.0 4.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 0.0 1.0 0.0
9 Brucella melitensis Brucellaceae 2.00 0.0 0.0 2.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 1.0 0.0
10 Brucella suis Brucellaceae 2.00 0.0 0.0 3.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 0.0 1.0 0.0
11 Campylobacter jejuni Campylobacteraceae 1.50 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 1.0
12 Clostridium perfringens Clostridiaceae 0.20 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0
13 Corynebacterium diphtheriae Corynebacteriaceae 2.00 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Helps NaN 0.0 0.0
14 Coxiella burnetii Coxiellaceae 8.00 0.0 0.0 3.0 Inahalation Respiratory 1.0 0.0 Noeffect 0.0 1.0 0.0
15 E coli EHEC Enterobacteriaceae 0.33 0.0 0.0 2.0 Ingestion Gastrointestinal 1.0 1.0 Helps 1.0 1.0 1.0
16 E coli EIEC Enterobacteriaceae 0.40 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 1.0
17 E coli EPEC Enterobacteriaceae 0.40 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0
18 E coli ETEC Enterobacteriaceae 0.33 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0
19 Haemophilus ducreyi Pasteurellaceae 1.80 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Helps 1.0 1.0 1.0
20 Helicobacter pylori Helicobacteraceae 2.40 1.0 0.0 2.0 Ingestion Gastrointestinal 0.0 NaN NaN 1.0 NaN 1.0
21 Legionella pneumophila Legionellaceae 3.30 0.0 1.0 1.0 Inahalation Respiratory 0.0 0.0 Noeffect 1.0 1.0 1.0
22 Listeria monocytogenes Listeriaceae 1.00 0.0 1.0 NaN Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 1.0 1.0
23 Mycobacterium tuberculosis Mycobacteriaceae 19.00 1.0 1.0 NaN Inahalation Respiratory 1.0 1.0 Helps 1.0 1.0 0.0
24 Neisseria gonorrhoeae Neisseriaceae 0.58 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 1.0 0.0
25 Neisseria meningitidis Neisseriaceae 0.72 1.0 1.0 1.0 Inahalation Respiratory 1.0 1.0 Noeffect 0.0 0.0 0.0
26 Orientia tsutsugamushi Rickettsiaceae 9.00 0.0 1.0 1.0 Vector Bloodstream 1.0 0.0 Noeffect 0.0 1.0 0.0
27 Plesiomonas shigelloides Enterobacteriaceae 0.43 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 NaN NaN 0.0 NaN 1.0
28 Rickettsia conorii (SFG) Rickettsiaceae 4.10 0.0 0.0 2.0 Vector Bloodstream 1.0 0.0 Noeffect NaN 1.0 0.0
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Noeffect NaN 1.0 0.0
30 Rickettsia rickettsii (SFG) Rickettsiaceae 9.00 0.0 1.0 1.0 Vector Bloodstream 1.0 0.0 Noeffect 1.0 1.0 0.0
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 1.0 1.0 1.0 Ingestion Gastrointestinal 1.0 1.0 Noeffect NaN 1.0 1.0
32 Salmonella enterica s. Typhimurium Enterobacteriaceae 0.40 1.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps NaN 1.0 1.0
33 Shigella dysenteriae Enterobacteriaceae 0.67 1.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 1.0
34 Shigella flexneri Enterobacteriaceae 0.68 1.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 0.0
35 Shigella sonnei Enterobacteriaceae 0.50 1.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 0.0
36 Staphylococcus aureus Staphylococcaceae 0.40 0.0 1.0 2.0 Ingestion Gastrointestinal 1.0 1.0 Noeffect 1.0 1.0 0.0
37 Streptococcus pneumoniae Streptococcaceae 0.50 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 0.0 0.0
38 Streptococcus pyogenes (group A) Streptococcaceae 0.40 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Noeffect 1.0 1.0 0.0
39 Treponema pallidum Spirochaetaceae 33.00 1.0 1.0 1.0 Sexual Genital 1.0 1.0 Helps 0.0 NaN 1.0
40 Vibrio cholerae Vibrionaceae 0.20 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0
41 Vibrio parahaemolyticus Vibrionaceae 0.20 0.0 0.0 2.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 1.0
42 Vibrio vulnificus Vibrionaceae 0.16 0.0 1.0 1.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 0.0 1.0
43 Yersinia enterocolitica Enterobacteriaceae 0.55 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0
44 Yersinia pestis Enterobacteriaceae 1.25 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Hinder 1.0 1.0 0.0
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0
46 Leptospira interrogans Spirochaetaceae 9.00 0.0 1.0 1.0 Direct Bloodstream 1.0 0.0 Noeffect 0.0 0.0 1.0
47 Bartonella henselae Bartonellaceae 3.00 0.0 0.0 3.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 1.0
48 Bartonella bacilliformis Bartonellaceae 24.00 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Noeffect 0.0 1.0 1.0
49 Bartonella quintana Bartonellaceae 3.00 0.0 0.0 4.0 Vector Bloodstream 1.0 1.0 Noeffect 0.0 0.0 NaN
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 1.0 0.0
51 Burkholderia pseudomallei Burkholderiaceae 1.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 1.0
52 Burkholderia mallei Burkholderiaceae 0.75 0.0 1.0 1.0 Direct Cutaneous 1.0 NaN Noeffect 0.0 1.0 0.0
53 Mycoplasma pneumoniae Mycoplasmataceae 6.00 1.0 0.0 4.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 1.0 1.0
54 Mycoplasma genitalium Mycoplasmataceae 12.00 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 0.0 1.0
55 Borrelia burgdorferi Spirochaetaceae 4.00 0.0 0.0 4.0 Vector Bloodstream 1.0 0.0 Noeffect 0.0 0.0 1.0
56 Chlamydia pneumoniae Chlamydiaceae 24.00 1.0 NaN 2.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 1.0 0.0
57 Clostridium difficile Peptostreptococcaceae 0.50 0.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0
58 Ehrlichia chaffeensis Anaplasmataceae 19.00 0.0 0.0 2.0 Vector Bloodstream 1.0 0.0 Noeffect NaN 1.0 0.0
59 Klebsiella granulomatis Enterobacteriaceae NaN 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders NaN 1.0 0.0
60 Mycobacterium leprae Mycobacteriaceae 240.00 0.0 1.0 2.0 Inahalation Respiratory 1.0 1.0 Noeffect 0.0 1.0 0.0
61 Francisella tularensis tularensis (Type A) Francisellaceae 3.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0
62 Francisella tularensis holarctica (Type B) Francisellaceae 3.00 0.0 0.0 4.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0
63 Mycobacterium bovis Mycobacteriaceae 23.00 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 1.0 0.0
64 Nocardia brasiliensis Nocardiaceae 3.00 0.0 0.0 3.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 1.0 0.0
65 Erysipelothrix rhusiopathiae Erysiopelotrichaceae NaN 0.0 0.0 2.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0
66 Mycobacterium marinum Mycobacteriaceae 24.00 0.0 0.0 3.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 1.0 0.0
67 Fusobacterium nucleatum Fusobacteriaceae 0.72 1.0 NaN NaN NaN Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 0.0
68 Haemophilus influenzae Type B Pasteurellaceae 0.50 1.0 NaN 2.0 Inahalation Respiratory 1.0 1.0 Helps 0.0 0.0 0.0
69 Pasteurella multocida Brucellaceae 48.00 0.0 0.0 2.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 0.0 0.0
70 Chlamydia psittaci Chlamydiaceae 24.00 0.0 0.0 2.0 Inahalation Respiratory 0.0 0.0 NaN 0.0 1.0 0.0
71 Clostridium tetani Clostridiaceae 0.50 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 0.0 1.0
72 Enterococcus faecalis Enterococcaceae 0.50 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0
73 Streptobacillus moniliformis Leptotrichiaceae 36.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect NaN NaN 0.0
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 0.0 0.0 3.0 Direct Cutaneous 1.0 NaN Noeffect 0.0 0.0 1.0
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 0.0 0.0 3.0 NaN NaN 1.0 0.0 Noeffect 0.0 0.0 1.0
76 Acinetobacter baumannii Moraxellaceae 0.66 0.0 0.0 3.0 Direct Cutaneous 1.0 1.0 Noeffect 0.0 0.0 0.0
In [6]:
bact['Family'].value_counts()
Out[6]:
Enterobacteriaceae       14
Brucellaceae              4
Mycobacteriaceae          4
Rickettsiaceae            4
Vibrionaceae              3
Spirochaetaceae           3
Chlamydiaceae             3
Bartonellaceae            3
Mycoplasmataceae          2
Streptococcaceae          2
Clostridiaceae            2
Burkholderiaceae          2
Francisellaceae           2
Pasteurellaceae           2
Neisseriaceae             2
Xanthomonadaceae          1
Leptotrichiaceae          1
Peptostreptococcaceae     1
Enterococcaceae           1
Nocardiaceae              1
Erysiopelotrichaceae      1
Pseudomonadaceae          1
Fusobacteriaceae          1
Anaplasmataceae           1
Aeromonadaceae            1
Staphylococcaceae         1
Anaplasmataceae           1
Listeriaceae              1
Legionellaceae            1
Helicobacteraceae         1
Coxiellaceae              1
Corynebacteriaceae        1
Campylobacteraceae        1
Alcaligenaceae            1
Bacteroidaceae            1
d                         1
Bacillaceae               1
Arcobacteraceae           1
Moraxellaceae             1
Name: Family, dtype: int64
In [7]:
bact['No.bacterial pathogen'] = bact['Family'].map(bact['Family'].value_counts())
bact
Out[7]:
Pathogen Family GT Endemic Severity Severity_Scale Route Tissue Sytemic Transmissibility Aid Immune_killing Immune_survival Motility No.bacterial pathogen
1 Aeromonas hydrophila Aeromonadaceae 0.35 0.0 0.0 2.0 Ingestion Gastrointestinal 0.0 0.0 Help 0.0 0.0 1.0 1
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 0.0 0.0 3.0 Vector Bloodstream 1.0 0.0 Hinders 0.0 1.0 0.0 1
3 Arcobacter butzleri Arcobacteraceae 0.66 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 1.0 1
4 Bacillus anthracis Bacillaceae 0.50 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 1.0 0.0 0.0 1
5 Bacillus cereus d 0.30 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 1.0 1
6 Bacteroides fragilis Bacteroidaceae 0.67 0.0 1.0 1.0 NaN Gastrointestinal 1.0 0.0 Noeffect 0.0 NaN 0.0 1
7 Bordatella pertussis Alcaligenaceae 3.80 1.0 NaN 2.0 Inahalation Respiratory 0.0 1.0 Helps 1.0 1.0 0.0 1
8 Brucella abortus Brucellaceae 2.00 0.0 0.0 4.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 0.0 1.0 0.0 4
9 Brucella melitensis Brucellaceae 2.00 0.0 0.0 2.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 1.0 0.0 4
10 Brucella suis Brucellaceae 2.00 0.0 0.0 3.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 0.0 1.0 0.0 4
11 Campylobacter jejuni Campylobacteraceae 1.50 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 1.0 1
12 Clostridium perfringens Clostridiaceae 0.20 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0 2
13 Corynebacterium diphtheriae Corynebacteriaceae 2.00 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Helps NaN 0.0 0.0 1
14 Coxiella burnetii Coxiellaceae 8.00 0.0 0.0 3.0 Inahalation Respiratory 1.0 0.0 Noeffect 0.0 1.0 0.0 1
15 E coli EHEC Enterobacteriaceae 0.33 0.0 0.0 2.0 Ingestion Gastrointestinal 1.0 1.0 Helps 1.0 1.0 1.0 14
16 E coli EIEC Enterobacteriaceae 0.40 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 1.0 14
17 E coli EPEC Enterobacteriaceae 0.40 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0 14
18 E coli ETEC Enterobacteriaceae 0.33 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0 14
19 Haemophilus ducreyi Pasteurellaceae 1.80 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Helps 1.0 1.0 1.0 2
20 Helicobacter pylori Helicobacteraceae 2.40 1.0 0.0 2.0 Ingestion Gastrointestinal 0.0 NaN NaN 1.0 NaN 1.0 1
21 Legionella pneumophila Legionellaceae 3.30 0.0 1.0 1.0 Inahalation Respiratory 0.0 0.0 Noeffect 1.0 1.0 1.0 1
22 Listeria monocytogenes Listeriaceae 1.00 0.0 1.0 NaN Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 1.0 1.0 1
23 Mycobacterium tuberculosis Mycobacteriaceae 19.00 1.0 1.0 NaN Inahalation Respiratory 1.0 1.0 Helps 1.0 1.0 0.0 4
24 Neisseria gonorrhoeae Neisseriaceae 0.58 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 1.0 0.0 2
25 Neisseria meningitidis Neisseriaceae 0.72 1.0 1.0 1.0 Inahalation Respiratory 1.0 1.0 Noeffect 0.0 0.0 0.0 2
26 Orientia tsutsugamushi Rickettsiaceae 9.00 0.0 1.0 1.0 Vector Bloodstream 1.0 0.0 Noeffect 0.0 1.0 0.0 4
27 Plesiomonas shigelloides Enterobacteriaceae 0.43 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 NaN NaN 0.0 NaN 1.0 14
28 Rickettsia conorii (SFG) Rickettsiaceae 4.10 0.0 0.0 2.0 Vector Bloodstream 1.0 0.0 Noeffect NaN 1.0 0.0 4
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Noeffect NaN 1.0 0.0 4
30 Rickettsia rickettsii (SFG) Rickettsiaceae 9.00 0.0 1.0 1.0 Vector Bloodstream 1.0 0.0 Noeffect 1.0 1.0 0.0 4
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 1.0 1.0 1.0 Ingestion Gastrointestinal 1.0 1.0 Noeffect NaN 1.0 1.0 14
32 Salmonella enterica s. Typhimurium Enterobacteriaceae 0.40 1.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps NaN 1.0 1.0 14
33 Shigella dysenteriae Enterobacteriaceae 0.67 1.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 1.0 14
34 Shigella flexneri Enterobacteriaceae 0.68 1.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 0.0 14
35 Shigella sonnei Enterobacteriaceae 0.50 1.0 0.0 4.0 Ingestion Gastrointestinal 0.0 1.0 Helps 1.0 1.0 0.0 14
36 Staphylococcus aureus Staphylococcaceae 0.40 0.0 1.0 2.0 Ingestion Gastrointestinal 1.0 1.0 Noeffect 1.0 1.0 0.0 1
37 Streptococcus pneumoniae Streptococcaceae 0.50 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 0.0 0.0 2
38 Streptococcus pyogenes (group A) Streptococcaceae 0.40 1.0 1.0 1.0 Inahalation Respiratory 0.0 1.0 Noeffect 1.0 1.0 0.0 2
39 Treponema pallidum Spirochaetaceae 33.00 1.0 1.0 1.0 Sexual Genital 1.0 1.0 Helps 0.0 NaN 1.0 3
40 Vibrio cholerae Vibrionaceae 0.20 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0 3
41 Vibrio parahaemolyticus Vibrionaceae 0.20 0.0 0.0 2.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 1.0 3
42 Vibrio vulnificus Vibrionaceae 0.16 0.0 1.0 1.0 Ingestion Gastrointestinal 1.0 0.0 Noeffect 1.0 0.0 1.0 3
43 Yersinia enterocolitica Enterobacteriaceae 0.55 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0 14
44 Yersinia pestis Enterobacteriaceae 1.25 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Hinder 1.0 1.0 0.0 14
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0 14
46 Leptospira interrogans Spirochaetaceae 9.00 0.0 1.0 1.0 Direct Bloodstream 1.0 0.0 Noeffect 0.0 0.0 1.0 3
47 Bartonella henselae Bartonellaceae 3.00 0.0 0.0 3.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 1.0 3
48 Bartonella bacilliformis Bartonellaceae 24.00 0.0 1.0 1.0 Vector Bloodstream 1.0 1.0 Noeffect 0.0 1.0 1.0 3
49 Bartonella quintana Bartonellaceae 3.00 0.0 0.0 4.0 Vector Bloodstream 1.0 1.0 Noeffect 0.0 0.0 NaN 3
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 1.0 0.0 3
51 Burkholderia pseudomallei Burkholderiaceae 1.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 1.0 2
52 Burkholderia mallei Burkholderiaceae 0.75 0.0 1.0 1.0 Direct Cutaneous 1.0 NaN Noeffect 0.0 1.0 0.0 2
53 Mycoplasma pneumoniae Mycoplasmataceae 6.00 1.0 0.0 4.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 1.0 1.0 2
54 Mycoplasma genitalium Mycoplasmataceae 12.00 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders 0.0 0.0 1.0 2
55 Borrelia burgdorferi Spirochaetaceae 4.00 0.0 0.0 4.0 Vector Bloodstream 1.0 0.0 Noeffect 0.0 0.0 1.0 3
56 Chlamydia pneumoniae Chlamydiaceae 24.00 1.0 NaN 2.0 Inahalation Respiratory 0.0 1.0 Helps 0.0 1.0 0.0 3
57 Clostridium difficile Peptostreptococcaceae 0.50 0.0 1.0 1.0 Ingestion Gastrointestinal 0.0 1.0 Helps 0.0 0.0 1.0 1
58 Ehrlichia chaffeensis Anaplasmataceae 19.00 0.0 0.0 2.0 Vector Bloodstream 1.0 0.0 Noeffect NaN 1.0 0.0 1
59 Klebsiella granulomatis Enterobacteriaceae NaN 1.0 0.0 4.0 Sexual Genital 0.0 1.0 Hinders NaN 1.0 0.0 14
60 Mycobacterium leprae Mycobacteriaceae 240.00 0.0 1.0 2.0 Inahalation Respiratory 1.0 1.0 Noeffect 0.0 1.0 0.0 4
61 Francisella tularensis tularensis (Type A) Francisellaceae 3.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0 2
62 Francisella tularensis holarctica (Type B) Francisellaceae 3.00 0.0 0.0 4.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0 2
63 Mycobacterium bovis Mycobacteriaceae 23.00 0.0 0.0 4.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 0.0 1.0 0.0 4
64 Nocardia brasiliensis Nocardiaceae 3.00 0.0 0.0 3.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 1.0 0.0 1
65 Erysipelothrix rhusiopathiae Erysiopelotrichaceae NaN 0.0 0.0 2.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 1.0 0.0 1
66 Mycobacterium marinum Mycobacteriaceae 24.00 0.0 0.0 3.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 1.0 0.0 4
67 Fusobacterium nucleatum Fusobacteriaceae 0.72 1.0 NaN NaN NaN Gastrointestinal 0.0 0.0 Noeffect 0.0 0.0 0.0 1
68 Haemophilus influenzae Type B Pasteurellaceae 0.50 1.0 NaN 2.0 Inahalation Respiratory 1.0 1.0 Helps 0.0 0.0 0.0 2
69 Pasteurella multocida Brucellaceae 48.00 0.0 0.0 2.0 Direct Cutaneous 0.0 0.0 Noeffect 0.0 0.0 0.0 4
70 Chlamydia psittaci Chlamydiaceae 24.00 0.0 0.0 2.0 Inahalation Respiratory 0.0 0.0 NaN 0.0 1.0 0.0 3
71 Clostridium tetani Clostridiaceae 0.50 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect 0.0 0.0 1.0 2
72 Enterococcus faecalis Enterococcaceae 0.50 0.0 0.0 3.0 Ingestion Gastrointestinal 0.0 0.0 Noeffect 1.0 1.0 0.0 1
73 Streptobacillus moniliformis Leptotrichiaceae 36.00 0.0 1.0 1.0 Direct Cutaneous 1.0 0.0 Noeffect NaN NaN 0.0 1
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 0.0 0.0 3.0 Direct Cutaneous 1.0 NaN Noeffect 0.0 0.0 1.0 1
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 0.0 0.0 3.0 NaN NaN 1.0 0.0 Noeffect 0.0 0.0 1.0 1
76 Acinetobacter baumannii Moraxellaceae 0.66 0.0 0.0 3.0 Direct Cutaneous 1.0 1.0 Noeffect 0.0 0.0 0.0 1
In [8]:
bact1 = pd.DataFrame(bact, columns=["Severity", "Family","No.bacterial pathogen"])
bact1
Out[8]:
Severity Family No.bacterial pathogen
1 0.0 Aeromonadaceae 1
2 0.0 Anaplasmataceae 1
3 0.0 Arcobacteraceae 1
4 1.0 Bacillaceae 1
5 0.0 d 1
6 1.0 Bacteroidaceae 1
7 NaN Alcaligenaceae 1
8 0.0 Brucellaceae 4
9 0.0 Brucellaceae 4
10 0.0 Brucellaceae 4
11 0.0 Campylobacteraceae 1
12 0.0 Clostridiaceae 2
13 1.0 Corynebacteriaceae 1
14 0.0 Coxiellaceae 1
15 0.0 Enterobacteriaceae 14
16 0.0 Enterobacteriaceae 14
17 0.0 Enterobacteriaceae 14
18 0.0 Enterobacteriaceae 14
19 0.0 Pasteurellaceae 2
20 0.0 Helicobacteraceae 1
21 1.0 Legionellaceae 1
22 1.0 Listeriaceae 1
23 1.0 Mycobacteriaceae 4
24 0.0 Neisseriaceae 2
25 1.0 Neisseriaceae 2
26 1.0 Rickettsiaceae 4
27 0.0 Enterobacteriaceae 14
28 0.0 Rickettsiaceae 4
29 1.0 Rickettsiaceae 4
30 1.0 Rickettsiaceae 4
31 1.0 Enterobacteriaceae 14
32 0.0 Enterobacteriaceae 14
33 1.0 Enterobacteriaceae 14
34 1.0 Enterobacteriaceae 14
35 0.0 Enterobacteriaceae 14
36 1.0 Staphylococcaceae 1
37 1.0 Streptococcaceae 2
38 1.0 Streptococcaceae 2
39 1.0 Spirochaetaceae 3
40 0.0 Vibrionaceae 3
41 0.0 Vibrionaceae 3
42 1.0 Vibrionaceae 3
43 0.0 Enterobacteriaceae 14
44 1.0 Enterobacteriaceae 14
45 0.0 Enterobacteriaceae 14
46 1.0 Spirochaetaceae 3
47 0.0 Bartonellaceae 3
48 1.0 Bartonellaceae 3
49 0.0 Bartonellaceae 3
50 0.0 Chlamydiaceae 3
51 1.0 Burkholderiaceae 2
52 1.0 Burkholderiaceae 2
53 0.0 Mycoplasmataceae 2
54 0.0 Mycoplasmataceae 2
55 0.0 Spirochaetaceae 3
56 NaN Chlamydiaceae 3
57 1.0 Peptostreptococcaceae 1
58 0.0 Anaplasmataceae 1
59 0.0 Enterobacteriaceae 14
60 1.0 Mycobacteriaceae 4
61 1.0 Francisellaceae 2
62 0.0 Francisellaceae 2
63 0.0 Mycobacteriaceae 4
64 0.0 Nocardiaceae 1
65 0.0 Erysiopelotrichaceae 1
66 0.0 Mycobacteriaceae 4
67 NaN Fusobacteriaceae 1
68 NaN Pasteurellaceae 2
69 0.0 Brucellaceae 4
70 0.0 Chlamydiaceae 3
71 1.0 Clostridiaceae 2
72 0.0 Enterococcaceae 1
73 1.0 Leptotrichiaceae 1
74 0.0 Pseudomonadaceae 1
75 0.0 Xanthomonadaceae 1
76 0.0 Moraxellaceae 1
In [9]:
bact1 = pd.DataFrame(bact, columns=["Severity", "Family","No.bacterial pathogen"])
bact1
Out[9]:
Severity Family No.bacterial pathogen
1 0.0 Aeromonadaceae 1
2 0.0 Anaplasmataceae 1
3 0.0 Arcobacteraceae 1
4 1.0 Bacillaceae 1
5 0.0 d 1
6 1.0 Bacteroidaceae 1
7 NaN Alcaligenaceae 1
8 0.0 Brucellaceae 4
9 0.0 Brucellaceae 4
10 0.0 Brucellaceae 4
11 0.0 Campylobacteraceae 1
12 0.0 Clostridiaceae 2
13 1.0 Corynebacteriaceae 1
14 0.0 Coxiellaceae 1
15 0.0 Enterobacteriaceae 14
16 0.0 Enterobacteriaceae 14
17 0.0 Enterobacteriaceae 14
18 0.0 Enterobacteriaceae 14
19 0.0 Pasteurellaceae 2
20 0.0 Helicobacteraceae 1
21 1.0 Legionellaceae 1
22 1.0 Listeriaceae 1
23 1.0 Mycobacteriaceae 4
24 0.0 Neisseriaceae 2
25 1.0 Neisseriaceae 2
26 1.0 Rickettsiaceae 4
27 0.0 Enterobacteriaceae 14
28 0.0 Rickettsiaceae 4
29 1.0 Rickettsiaceae 4
30 1.0 Rickettsiaceae 4
31 1.0 Enterobacteriaceae 14
32 0.0 Enterobacteriaceae 14
33 1.0 Enterobacteriaceae 14
34 1.0 Enterobacteriaceae 14
35 0.0 Enterobacteriaceae 14
36 1.0 Staphylococcaceae 1
37 1.0 Streptococcaceae 2
38 1.0 Streptococcaceae 2
39 1.0 Spirochaetaceae 3
40 0.0 Vibrionaceae 3
41 0.0 Vibrionaceae 3
42 1.0 Vibrionaceae 3
43 0.0 Enterobacteriaceae 14
44 1.0 Enterobacteriaceae 14
45 0.0 Enterobacteriaceae 14
46 1.0 Spirochaetaceae 3
47 0.0 Bartonellaceae 3
48 1.0 Bartonellaceae 3
49 0.0 Bartonellaceae 3
50 0.0 Chlamydiaceae 3
51 1.0 Burkholderiaceae 2
52 1.0 Burkholderiaceae 2
53 0.0 Mycoplasmataceae 2
54 0.0 Mycoplasmataceae 2
55 0.0 Spirochaetaceae 3
56 NaN Chlamydiaceae 3
57 1.0 Peptostreptococcaceae 1
58 0.0 Anaplasmataceae 1
59 0.0 Enterobacteriaceae 14
60 1.0 Mycobacteriaceae 4
61 1.0 Francisellaceae 2
62 0.0 Francisellaceae 2
63 0.0 Mycobacteriaceae 4
64 0.0 Nocardiaceae 1
65 0.0 Erysiopelotrichaceae 1
66 0.0 Mycobacteriaceae 4
67 NaN Fusobacteriaceae 1
68 NaN Pasteurellaceae 2
69 0.0 Brucellaceae 4
70 0.0 Chlamydiaceae 3
71 1.0 Clostridiaceae 2
72 0.0 Enterococcaceae 1
73 1.0 Leptotrichiaceae 1
74 0.0 Pseudomonadaceae 1
75 0.0 Xanthomonadaceae 1
76 0.0 Moraxellaceae 1
In [10]:
replace_dict= {0:'Nonsevere',1:'Severe'}
print(replace_dict)

{0: 'Nonsevere', 1: 'Severe'}
In [11]:
bact1['Severity']=bact['Severity'].map(replace_dict)
bact1
Out[11]:
Severity Family No.bacterial pathogen
1 Nonsevere Aeromonadaceae 1
2 Nonsevere Anaplasmataceae 1
3 Nonsevere Arcobacteraceae 1
4 Severe Bacillaceae 1
5 Nonsevere d 1
6 Severe Bacteroidaceae 1
7 NaN Alcaligenaceae 1
8 Nonsevere Brucellaceae 4
9 Nonsevere Brucellaceae 4
10 Nonsevere Brucellaceae 4
11 Nonsevere Campylobacteraceae 1
12 Nonsevere Clostridiaceae 2
13 Severe Corynebacteriaceae 1
14 Nonsevere Coxiellaceae 1
15 Nonsevere Enterobacteriaceae 14
16 Nonsevere Enterobacteriaceae 14
17 Nonsevere Enterobacteriaceae 14
18 Nonsevere Enterobacteriaceae 14
19 Nonsevere Pasteurellaceae 2
20 Nonsevere Helicobacteraceae 1
21 Severe Legionellaceae 1
22 Severe Listeriaceae 1
23 Severe Mycobacteriaceae 4
24 Nonsevere Neisseriaceae 2
25 Severe Neisseriaceae 2
26 Severe Rickettsiaceae 4
27 Nonsevere Enterobacteriaceae 14
28 Nonsevere Rickettsiaceae 4
29 Severe Rickettsiaceae 4
30 Severe Rickettsiaceae 4
31 Severe Enterobacteriaceae 14
32 Nonsevere Enterobacteriaceae 14
33 Severe Enterobacteriaceae 14
34 Severe Enterobacteriaceae 14
35 Nonsevere Enterobacteriaceae 14
36 Severe Staphylococcaceae 1
37 Severe Streptococcaceae 2
38 Severe Streptococcaceae 2
39 Severe Spirochaetaceae 3
40 Nonsevere Vibrionaceae 3
41 Nonsevere Vibrionaceae 3
42 Severe Vibrionaceae 3
43 Nonsevere Enterobacteriaceae 14
44 Severe Enterobacteriaceae 14
45 Nonsevere Enterobacteriaceae 14
46 Severe Spirochaetaceae 3
47 Nonsevere Bartonellaceae 3
48 Severe Bartonellaceae 3
49 Nonsevere Bartonellaceae 3
50 Nonsevere Chlamydiaceae 3
51 Severe Burkholderiaceae 2
52 Severe Burkholderiaceae 2
53 Nonsevere Mycoplasmataceae 2
54 Nonsevere Mycoplasmataceae 2
55 Nonsevere Spirochaetaceae 3
56 NaN Chlamydiaceae 3
57 Severe Peptostreptococcaceae 1
58 Nonsevere Anaplasmataceae 1
59 Nonsevere Enterobacteriaceae 14
60 Severe Mycobacteriaceae 4
61 Severe Francisellaceae 2
62 Nonsevere Francisellaceae 2
63 Nonsevere Mycobacteriaceae 4
64 Nonsevere Nocardiaceae 1
65 Nonsevere Erysiopelotrichaceae 1
66 Nonsevere Mycobacteriaceae 4
67 NaN Fusobacteriaceae 1
68 NaN Pasteurellaceae 2
69 Nonsevere Brucellaceae 4
70 Nonsevere Chlamydiaceae 3
71 Severe Clostridiaceae 2
72 Nonsevere Enterococcaceae 1
73 Severe Leptotrichiaceae 1
74 Nonsevere Pseudomonadaceae 1
75 Nonsevere Xanthomonadaceae 1
76 Nonsevere Moraxellaceae 1
In [12]:
bact2=pd.crosstab(bact1.Family,bact1.Severity)
bact2
Out[12]:
Severity Nonsevere Severe
Family
Aeromonadaceae 1 0
Anaplasmataceae 1 0
Anaplasmataceae 1 0
Arcobacteraceae 1 0
Bacillaceae 0 1
Bacteroidaceae 0 1
Bartonellaceae 2 1
Brucellaceae 4 0
Burkholderiaceae 0 2
Campylobacteraceae 1 0
Chlamydiaceae 2 0
Clostridiaceae 1 1
Corynebacteriaceae 0 1
Coxiellaceae 1 0
Enterobacteriaceae 10 4
Enterococcaceae 1 0
Erysiopelotrichaceae 1 0
Francisellaceae 1 1
Helicobacteraceae 1 0
Legionellaceae 0 1
Leptotrichiaceae 0 1
Listeriaceae 0 1
Moraxellaceae 1 0
Mycobacteriaceae 2 2
Mycoplasmataceae 2 0
Neisseriaceae 1 1
Nocardiaceae 1 0
Pasteurellaceae 1 0
Peptostreptococcaceae 0 1
Pseudomonadaceae 1 0
Rickettsiaceae 1 3
Spirochaetaceae 1 2
Staphylococcaceae 0 1
Streptococcaceae 0 2
Vibrionaceae 2 1
Xanthomonadaceae 1 0
d 1 0
In [13]:
sum(bact2.Nonsevere)
Out[13]:
44
In [14]:
sum(bact2.Severe)
Out[14]:
28
In [15]:
import matplotlib.pyplot as plt
bact2.plot(kind='bar', stacked=True,figsize=(19.5,6.5))
plt.title("Measure of Virluence 1")
plt.xlabel("Family")
plt.ylabel("No.Bacterial Species")
Out[15]:
Text(0, 0.5, 'No.Bacterial Species')
In [16]:
bact3 = pd.DataFrame(bact, columns=["Severity_Scale", "Family","No.bacterial pathogen"])
bact3
Out[16]:
Severity_Scale Family No.bacterial pathogen
1 2.0 Aeromonadaceae 1
2 3.0 Anaplasmataceae 1
3 4.0 Arcobacteraceae 1
4 1.0 Bacillaceae 1
5 4.0 d 1
6 1.0 Bacteroidaceae 1
7 2.0 Alcaligenaceae 1
8 4.0 Brucellaceae 4
9 2.0 Brucellaceae 4
10 3.0 Brucellaceae 4
11 4.0 Campylobacteraceae 1
12 4.0 Clostridiaceae 2
13 1.0 Corynebacteriaceae 1
14 3.0 Coxiellaceae 1
15 2.0 Enterobacteriaceae 14
16 4.0 Enterobacteriaceae 14
17 3.0 Enterobacteriaceae 14
18 3.0 Enterobacteriaceae 14
19 4.0 Pasteurellaceae 2
20 2.0 Helicobacteraceae 1
21 1.0 Legionellaceae 1
22 NaN Listeriaceae 1
23 NaN Mycobacteriaceae 4
24 4.0 Neisseriaceae 2
25 1.0 Neisseriaceae 2
26 1.0 Rickettsiaceae 4
27 3.0 Enterobacteriaceae 14
28 2.0 Rickettsiaceae 4
29 1.0 Rickettsiaceae 4
30 1.0 Rickettsiaceae 4
31 1.0 Enterobacteriaceae 14
32 4.0 Enterobacteriaceae 14
33 1.0 Enterobacteriaceae 14
34 1.0 Enterobacteriaceae 14
35 4.0 Enterobacteriaceae 14
36 2.0 Staphylococcaceae 1
37 1.0 Streptococcaceae 2
38 1.0 Streptococcaceae 2
39 1.0 Spirochaetaceae 3
40 3.0 Vibrionaceae 3
41 2.0 Vibrionaceae 3
42 1.0 Vibrionaceae 3
43 3.0 Enterobacteriaceae 14
44 1.0 Enterobacteriaceae 14
45 3.0 Enterobacteriaceae 14
46 1.0 Spirochaetaceae 3
47 3.0 Bartonellaceae 3
48 1.0 Bartonellaceae 3
49 4.0 Bartonellaceae 3
50 4.0 Chlamydiaceae 3
51 1.0 Burkholderiaceae 2
52 1.0 Burkholderiaceae 2
53 4.0 Mycoplasmataceae 2
54 4.0 Mycoplasmataceae 2
55 4.0 Spirochaetaceae 3
56 2.0 Chlamydiaceae 3
57 1.0 Peptostreptococcaceae 1
58 2.0 Anaplasmataceae 1
59 4.0 Enterobacteriaceae 14
60 2.0 Mycobacteriaceae 4
61 1.0 Francisellaceae 2
62 4.0 Francisellaceae 2
63 4.0 Mycobacteriaceae 4
64 3.0 Nocardiaceae 1
65 2.0 Erysiopelotrichaceae 1
66 3.0 Mycobacteriaceae 4
67 NaN Fusobacteriaceae 1
68 2.0 Pasteurellaceae 2
69 2.0 Brucellaceae 4
70 2.0 Chlamydiaceae 3
71 1.0 Clostridiaceae 2
72 3.0 Enterococcaceae 1
73 1.0 Leptotrichiaceae 1
74 3.0 Pseudomonadaceae 1
75 3.0 Xanthomonadaceae 1
76 3.0 Moraxellaceae 1
In [17]:
replace_dict1= {1:'Mostsevere',2:'MoreSevere',3:'Severe',4:'LeastSevere'}
print(replace_dict1)

{1: 'Mostsevere', 2: 'MoreSevere', 3: 'Severe', 4: 'LeastSevere'}
In [18]:
bact3['Severity_Scale']=bact['Severity_Scale'].map(replace_dict1)
bact3
Out[18]:
Severity_Scale Family No.bacterial pathogen
1 MoreSevere Aeromonadaceae 1
2 Severe Anaplasmataceae 1
3 LeastSevere Arcobacteraceae 1
4 Mostsevere Bacillaceae 1
5 LeastSevere d 1
6 Mostsevere Bacteroidaceae 1
7 MoreSevere Alcaligenaceae 1
8 LeastSevere Brucellaceae 4
9 MoreSevere Brucellaceae 4
10 Severe Brucellaceae 4
11 LeastSevere Campylobacteraceae 1
12 LeastSevere Clostridiaceae 2
13 Mostsevere Corynebacteriaceae 1
14 Severe Coxiellaceae 1
15 MoreSevere Enterobacteriaceae 14
16 LeastSevere Enterobacteriaceae 14
17 Severe Enterobacteriaceae 14
18 Severe Enterobacteriaceae 14
19 LeastSevere Pasteurellaceae 2
20 MoreSevere Helicobacteraceae 1
21 Mostsevere Legionellaceae 1
22 NaN Listeriaceae 1
23 NaN Mycobacteriaceae 4
24 LeastSevere Neisseriaceae 2
25 Mostsevere Neisseriaceae 2
26 Mostsevere Rickettsiaceae 4
27 Severe Enterobacteriaceae 14
28 MoreSevere Rickettsiaceae 4
29 Mostsevere Rickettsiaceae 4
30 Mostsevere Rickettsiaceae 4
31 Mostsevere Enterobacteriaceae 14
32 LeastSevere Enterobacteriaceae 14
33 Mostsevere Enterobacteriaceae 14
34 Mostsevere Enterobacteriaceae 14
35 LeastSevere Enterobacteriaceae 14
36 MoreSevere Staphylococcaceae 1
37 Mostsevere Streptococcaceae 2
38 Mostsevere Streptococcaceae 2
39 Mostsevere Spirochaetaceae 3
40 Severe Vibrionaceae 3
41 MoreSevere Vibrionaceae 3
42 Mostsevere Vibrionaceae 3
43 Severe Enterobacteriaceae 14
44 Mostsevere Enterobacteriaceae 14
45 Severe Enterobacteriaceae 14
46 Mostsevere Spirochaetaceae 3
47 Severe Bartonellaceae 3
48 Mostsevere Bartonellaceae 3
49 LeastSevere Bartonellaceae 3
50 LeastSevere Chlamydiaceae 3
51 Mostsevere Burkholderiaceae 2
52 Mostsevere Burkholderiaceae 2
53 LeastSevere Mycoplasmataceae 2
54 LeastSevere Mycoplasmataceae 2
55 LeastSevere Spirochaetaceae 3
56 MoreSevere Chlamydiaceae 3
57 Mostsevere Peptostreptococcaceae 1
58 MoreSevere Anaplasmataceae 1
59 LeastSevere Enterobacteriaceae 14
60 MoreSevere Mycobacteriaceae 4
61 Mostsevere Francisellaceae 2
62 LeastSevere Francisellaceae 2
63 LeastSevere Mycobacteriaceae 4
64 Severe Nocardiaceae 1
65 MoreSevere Erysiopelotrichaceae 1
66 Severe Mycobacteriaceae 4
67 NaN Fusobacteriaceae 1
68 MoreSevere Pasteurellaceae 2
69 MoreSevere Brucellaceae 4
70 MoreSevere Chlamydiaceae 3
71 Mostsevere Clostridiaceae 2
72 Severe Enterococcaceae 1
73 Mostsevere Leptotrichiaceae 1
74 Severe Pseudomonadaceae 1
75 Severe Xanthomonadaceae 1
76 Severe Moraxellaceae 1
In [19]:
bact4=pd.crosstab(bact3.Family,bact3.Severity_Scale)
bact4
Out[19]:
Severity_Scale LeastSevere MoreSevere Mostsevere Severe
Family
Aeromonadaceae 0 1 0 0
Alcaligenaceae 0 1 0 0
Anaplasmataceae 0 1 0 0
Anaplasmataceae 0 0 0 1
Arcobacteraceae 1 0 0 0
Bacillaceae 0 0 1 0
Bacteroidaceae 0 0 1 0
Bartonellaceae 1 0 1 1
Brucellaceae 1 2 0 1
Burkholderiaceae 0 0 2 0
Campylobacteraceae 1 0 0 0
Chlamydiaceae 1 2 0 0
Clostridiaceae 1 0 1 0
Corynebacteriaceae 0 0 1 0
Coxiellaceae 0 0 0 1
Enterobacteriaceae 4 1 4 5
Enterococcaceae 0 0 0 1
Erysiopelotrichaceae 0 1 0 0
Francisellaceae 1 0 1 0
Helicobacteraceae 0 1 0 0
Legionellaceae 0 0 1 0
Leptotrichiaceae 0 0 1 0
Moraxellaceae 0 0 0 1
Mycobacteriaceae 1 1 0 1
Mycoplasmataceae 2 0 0 0
Neisseriaceae 1 0 1 0
Nocardiaceae 0 0 0 1
Pasteurellaceae 1 1 0 0
Peptostreptococcaceae 0 0 1 0
Pseudomonadaceae 0 0 0 1
Rickettsiaceae 0 1 3 0
Spirochaetaceae 1 0 2 0
Staphylococcaceae 0 1 0 0
Streptococcaceae 0 0 2 0
Vibrionaceae 0 1 1 1
Xanthomonadaceae 0 0 0 1
d 1 0 0 0
In [20]:
sum(bact4.LeastSevere)
Out[20]:
18
In [21]:
sum(bact4.Severe)
Out[21]:
16
In [22]:
sum(bact4.MoreSevere)
Out[22]:
15
In [23]:
sum(bact4.Mostsevere)
Out[23]:
24
In [24]:
bact4.plot(kind='bar', stacked=True,figsize=(19.5,6.5))
plt.title("Measure of Virluence 2")
plt.xlabel("Family ")
plt.ylabel("No.Bacterial Species")
Out[24]:
Text(0, 0.5, 'No.Bacterial Species')
In [ ]:
In [25]:
replace_dict2= {0:'NonEndemic',1:'Endemic'}
print(replace_dict2)
replace_dict3= {0:'Nonsystemic',1:'Systemic'}
print(replace_dict3)
replace_dict4= {0:'Nontransmissable',1:'Transmissable'}
print(replace_dict4)
replace_dict5= {0:'Motile',1:'Nonmotile'}
print(replace_dict5)

{0: 'NonEndemic', 1: 'Endemic'}
{0: 'Nonsystemic', 1: 'Systemic'}
{0: 'Nontransmissable', 1: 'Transmissable'}
{0: 'Motile', 1: 'Nonmotile'}
In [26]:
bact['Severity']=bact['Severity'].map(replace_dict)
bact['Severity_Scale']=bact['Severity_Scale'].map(replace_dict1)
bact['Endemic']=bact['Endemic'].map(replace_dict2)
bact['Sytemic']=bact['Sytemic'].map(replace_dict3)
bact['Transmissibility']=bact['Transmissibility'].map(replace_dict4)
bact['Motility']=bact['Motility'].map(replace_dict5)
bact
Out[26]:
Pathogen Family GT Endemic Severity Severity_Scale Route Tissue Sytemic Transmissibility Aid Immune_killing Immune_survival Motility No.bacterial pathogen
1 Aeromonas hydrophila Aeromonadaceae 0.35 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Help 0.0 0.0 Nonmotile 1
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.0 1.0 Motile 1
3 Arcobacter butzleri Arcobacteraceae 0.66 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.0 0.0 Nonmotile 1
4 Bacillus anthracis Bacillaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 1.0 0.0 Motile 1
5 Bacillus cereus d 0.30 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.0 1.0 Nonmotile 1
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere NaN Gastrointestinal Systemic Nontransmissable Noeffect 0.0 NaN Motile 1
7 Bordatella pertussis Alcaligenaceae 3.80 Endemic NaN MoreSevere Inahalation Respiratory Nonsystemic Transmissable Helps 1.0 1.0 Motile 1
8 Brucella abortus Brucellaceae 2.00 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.0 1.0 Motile 4
9 Brucella melitensis Brucellaceae 2.00 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.0 1.0 Motile 4
10 Brucella suis Brucellaceae 2.00 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.0 1.0 Motile 4
11 Campylobacter jejuni Campylobacteraceae 1.50 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.0 1.0 Nonmotile 1
12 Clostridium perfringens Clostridiaceae 0.20 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.0 1.0 Motile 2
13 Corynebacterium diphtheriae Corynebacteriaceae 2.00 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps NaN 0.0 Motile 1
14 Coxiella burnetii Coxiellaceae 8.00 NonEndemic Nonsevere Severe Inahalation Respiratory Systemic Nontransmissable Noeffect 0.0 1.0 Motile 1
15 E coli EHEC Enterobacteriaceae 0.33 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Systemic Transmissable Helps 1.0 1.0 Nonmotile 14
16 E coli EIEC Enterobacteriaceae 0.40 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.0 1.0 Nonmotile 14
17 E coli EPEC Enterobacteriaceae 0.40 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.0 0.0 Nonmotile 14
18 E coli ETEC Enterobacteriaceae 0.33 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.0 0.0 Nonmotile 14
19 Haemophilus ducreyi Pasteurellaceae 1.80 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Helps 1.0 1.0 Nonmotile 2
20 Helicobacter pylori Helicobacteraceae 2.40 Endemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic NaN NaN 1.0 NaN Nonmotile 1
21 Legionella pneumophila Legionellaceae 3.30 NonEndemic Severe Mostsevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 1.0 1.0 Nonmotile 1
22 Listeria monocytogenes Listeriaceae 1.00 NonEndemic Severe NaN Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.0 1.0 Nonmotile 1
23 Mycobacterium tuberculosis Mycobacteriaceae 19.00 Endemic Severe NaN Inahalation Respiratory Systemic Transmissable Helps 1.0 1.0 Motile 4
24 Neisseria gonorrhoeae Neisseriaceae 0.58 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.0 1.0 Motile 2
25 Neisseria meningitidis Neisseriaceae 0.72 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Noeffect 0.0 0.0 Motile 2
26 Orientia tsutsugamushi Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.0 1.0 Motile 4
27 Plesiomonas shigelloides Enterobacteriaceae 0.43 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic NaN NaN 0.0 NaN Nonmotile 14
28 Rickettsia conorii (SFG) Rickettsiaceae 4.10 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect NaN 1.0 Motile 4
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect NaN 1.0 Motile 4
30 Rickettsia rickettsii (SFG) Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 1.0 1.0 Motile 4
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 Endemic Severe Mostsevere Ingestion Gastrointestinal Systemic Transmissable Noeffect NaN 1.0 Nonmotile 14
32 Salmonella enterica s. Typhimurium Enterobacteriaceae 0.40 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps NaN 1.0 Nonmotile 14
33 Shigella dysenteriae Enterobacteriaceae 0.67 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.0 1.0 Nonmotile 14
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.0 1.0 Motile 14
35 Shigella sonnei Enterobacteriaceae 0.50 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.0 1.0 Motile 14
36 Staphylococcus aureus Staphylococcaceae 0.40 NonEndemic Severe MoreSevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.0 1.0 Motile 1
37 Streptococcus pneumoniae Streptococcaceae 0.50 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.0 0.0 Motile 2
38 Streptococcus pyogenes (group A) Streptococcaceae 0.40 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Noeffect 1.0 1.0 Motile 2
39 Treponema pallidum Spirochaetaceae 33.00 Endemic Severe Mostsevere Sexual Genital Systemic Transmissable Helps 0.0 NaN Nonmotile 3
40 Vibrio cholerae Vibrionaceae 0.20 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.0 0.0 Nonmotile 3
41 Vibrio parahaemolyticus Vibrionaceae 0.20 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.0 0.0 Nonmotile 3
42 Vibrio vulnificus Vibrionaceae 0.16 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.0 0.0 Nonmotile 3
43 Yersinia enterocolitica Enterobacteriaceae 0.55 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.0 1.0 Motile 14
44 Yersinia pestis Enterobacteriaceae 1.25 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Hinder 1.0 1.0 Motile 14
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.0 1.0 Motile 14
46 Leptospira interrogans Spirochaetaceae 9.00 NonEndemic Severe Mostsevere Direct Bloodstream Systemic Nontransmissable Noeffect 0.0 0.0 Nonmotile 3
47 Bartonella henselae Bartonellaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.0 1.0 Nonmotile 3
48 Bartonella bacilliformis Bartonellaceae 24.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.0 1.0 Nonmotile 3
49 Bartonella quintana Bartonellaceae 3.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Transmissable Noeffect 0.0 0.0 NaN 3
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.0 1.0 Motile 3
51 Burkholderia pseudomallei Burkholderiaceae 1.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.0 1.0 Nonmotile 2
52 Burkholderia mallei Burkholderiaceae 0.75 NonEndemic Severe Mostsevere Direct Cutaneous Systemic NaN Noeffect 0.0 1.0 Motile 2
53 Mycoplasma pneumoniae Mycoplasmataceae 6.00 Endemic Nonsevere LeastSevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.0 1.0 Nonmotile 2
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.0 0.0 Nonmotile 2
55 Borrelia burgdorferi Spirochaetaceae 4.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.0 0.0 Nonmotile 3
56 Chlamydia pneumoniae Chlamydiaceae 24.00 Endemic NaN MoreSevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.0 1.0 Motile 3
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.0 0.0 Nonmotile 1
58 Ehrlichia chaffeensis Anaplasmataceae 19.00 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect NaN 1.0 Motile 1
59 Klebsiella granulomatis Enterobacteriaceae NaN Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders NaN 1.0 Motile 14
60 Mycobacterium leprae Mycobacteriaceae 240.00 NonEndemic Severe MoreSevere Inahalation Respiratory Systemic Transmissable Noeffect 0.0 1.0 Motile 4
61 Francisella tularensis tularensis (Type A) Francisellaceae 3.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.0 1.0 Motile 2
62 Francisella tularensis holarctica (Type B) Francisellaceae 3.00 NonEndemic Nonsevere LeastSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.0 1.0 Motile 2
63 Mycobacterium bovis Mycobacteriaceae 23.00 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.0 1.0 Motile 4
64 Nocardia brasiliensis Nocardiaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.0 1.0 Motile 1
65 Erysipelothrix rhusiopathiae Erysiopelotrichaceae NaN NonEndemic Nonsevere MoreSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.0 1.0 Motile 1
66 Mycobacterium marinum Mycobacteriaceae 24.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.0 1.0 Motile 4
67 Fusobacterium nucleatum Fusobacteriaceae 0.72 Endemic NaN NaN NaN Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.0 0.0 Motile 1
68 Haemophilus influenzae Type B Pasteurellaceae 0.50 Endemic NaN MoreSevere Inahalation Respiratory Systemic Transmissable Helps 0.0 0.0 Motile 2
69 Pasteurella multocida Brucellaceae 48.00 NonEndemic Nonsevere MoreSevere Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.0 0.0 Motile 4
70 Chlamydia psittaci Chlamydiaceae 24.00 NonEndemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Nontransmissable NaN 0.0 1.0 Motile 3
71 Clostridium tetani Clostridiaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.0 0.0 Nonmotile 2
72 Enterococcus faecalis Enterococcaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.0 1.0 Motile 1
73 Streptobacillus moniliformis Leptotrichiaceae 36.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect NaN NaN Motile 1
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic NaN Noeffect 0.0 0.0 Nonmotile 1
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 NonEndemic Nonsevere Severe NaN NaN Systemic Nontransmissable Noeffect 0.0 0.0 Nonmotile 1
76 Acinetobacter baumannii Moraxellaceae 0.66 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Transmissable Noeffect 0.0 0.0 Motile 1
In [27]:
print(bact.isnull().sum())

Pathogen                 0
Family                   0
GT                       2
Endemic                  0
Severity                 4
Severity_Scale           3
Route                    3
Tissue                   1
Sytemic                  0
Transmissibility         4
Aid                      3
Immune_killing           8
Immune_survival          5
Motility                 1
No.bacterial pathogen    0
dtype: int64
In [28]:
bact_1 = bact.interpolate() 
bact_new = bact_1.apply(lambda x: x.fillna(x.value_counts().index[0]))
bact_new
Out[28]:
Pathogen Family GT Endemic Severity Severity_Scale Route Tissue Sytemic Transmissibility Aid Immune_killing Immune_survival Motility No.bacterial pathogen
1 Aeromonas hydrophila Aeromonadaceae 0.35 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Help 0.000000 0.0 Nonmotile 1
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
3 Arcobacter butzleri Arcobacteraceae 0.66 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
4 Bacillus anthracis Bacillaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 1.000000 0.0 Motile 1
5 Bacillus cereus d 0.30 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
7 Bordatella pertussis Alcaligenaceae 3.80 Endemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Transmissable Helps 1.000000 1.0 Motile 1
8 Brucella abortus Brucellaceae 2.00 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
9 Brucella melitensis Brucellaceae 2.00 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 1.0 Motile 4
10 Brucella suis Brucellaceae 2.00 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
11 Campylobacter jejuni Campylobacteraceae 1.50 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
12 Clostridium perfringens Clostridiaceae 0.20 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 2
13 Corynebacterium diphtheriae Corynebacteriaceae 2.00 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.500000 0.0 Motile 1
14 Coxiella burnetii Coxiellaceae 8.00 NonEndemic Nonsevere Severe Inahalation Respiratory Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
15 E coli EHEC Enterobacteriaceae 0.33 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Systemic Transmissable Helps 1.000000 1.0 Nonmotile 14
16 E coli EIEC Enterobacteriaceae 0.40 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
17 E coli EPEC Enterobacteriaceae 0.40 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 14
18 E coli ETEC Enterobacteriaceae 0.33 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 14
19 Haemophilus ducreyi Pasteurellaceae 1.80 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 2
20 Helicobacter pylori Helicobacteraceae 2.40 Endemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
21 Legionella pneumophila Legionellaceae 3.30 NonEndemic Severe Mostsevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
22 Listeria monocytogenes Listeriaceae 1.00 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
23 Mycobacterium tuberculosis Mycobacteriaceae 19.00 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Helps 1.000000 1.0 Motile 4
24 Neisseria gonorrhoeae Neisseriaceae 0.58 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 2
25 Neisseria meningitidis Neisseriaceae 0.72 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Noeffect 0.000000 0.0 Motile 2
26 Orientia tsutsugamushi Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
27 Plesiomonas shigelloides Enterobacteriaceae 0.43 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 14
28 Rickettsia conorii (SFG) Rickettsiaceae 4.10 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.333333 1.0 Motile 4
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.666667 1.0 Motile 4
30 Rickettsia rickettsii (SFG) Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 1.000000 1.0 Motile 4
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 Endemic Severe Mostsevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Nonmotile 14
32 Salmonella enterica s. Typhimurium Enterobacteriaceae 0.40 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
33 Shigella dysenteriae Enterobacteriaceae 0.67 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
35 Shigella sonnei Enterobacteriaceae 0.50 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
36 Staphylococcus aureus Staphylococcaceae 0.40 NonEndemic Severe MoreSevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Motile 1
37 Streptococcus pneumoniae Streptococcaceae 0.50 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.000000 0.0 Motile 2
38 Streptococcus pyogenes (group A) Streptococcaceae 0.40 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Noeffect 1.000000 1.0 Motile 2
39 Treponema pallidum Spirochaetaceae 33.00 Endemic Severe Mostsevere Sexual Genital Systemic Transmissable Helps 0.000000 0.5 Nonmotile 3
40 Vibrio cholerae Vibrionaceae 0.20 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 3
41 Vibrio parahaemolyticus Vibrionaceae 0.20 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
42 Vibrio vulnificus Vibrionaceae 0.16 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 0.0 Nonmotile 3
43 Yersinia enterocolitica Enterobacteriaceae 0.55 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 14
44 Yersinia pestis Enterobacteriaceae 1.25 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Hinder 1.000000 1.0 Motile 14
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 14
46 Leptospira interrogans Spirochaetaceae 9.00 NonEndemic Severe Mostsevere Direct Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
47 Bartonella henselae Bartonellaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 3
48 Bartonella bacilliformis Bartonellaceae 24.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.000000 1.0 Nonmotile 3
49 Bartonella quintana Bartonellaceae 3.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Transmissable Noeffect 0.000000 0.0 Motile 3
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 3
51 Burkholderia pseudomallei Burkholderiaceae 1.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 2
52 Burkholderia mallei Burkholderiaceae 0.75 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
53 Mycoplasma pneumoniae Mycoplasmataceae 6.00 Endemic Nonsevere LeastSevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.000000 1.0 Nonmotile 2
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 0.0 Nonmotile 2
55 Borrelia burgdorferi Spirochaetaceae 4.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
56 Chlamydia pneumoniae Chlamydiaceae 24.00 Endemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.000000 1.0 Motile 3
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
58 Ehrlichia chaffeensis Anaplasmataceae 19.00 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
59 Klebsiella granulomatis Enterobacteriaceae 129.50 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 14
60 Mycobacterium leprae Mycobacteriaceae 240.00 NonEndemic Severe MoreSevere Inahalation Respiratory Systemic Transmissable Noeffect 0.000000 1.0 Motile 4
61 Francisella tularensis tularensis (Type A) Francisellaceae 3.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
62 Francisella tularensis holarctica (Type B) Francisellaceae 3.00 NonEndemic Nonsevere LeastSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
63 Mycobacterium bovis Mycobacteriaceae 23.00 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
64 Nocardia brasiliensis Nocardiaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
65 Erysipelothrix rhusiopathiae Erysiopelotrichaceae 13.50 NonEndemic Nonsevere MoreSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
66 Mycobacterium marinum Mycobacteriaceae 24.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
67 Fusobacterium nucleatum Fusobacteriaceae 0.72 Endemic Nonsevere Mostsevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Motile 1
68 Haemophilus influenzae Type B Pasteurellaceae 0.50 Endemic Nonsevere MoreSevere Inahalation Respiratory Systemic Transmissable Helps 0.000000 0.0 Motile 2
69 Pasteurella multocida Brucellaceae 48.00 NonEndemic Nonsevere MoreSevere Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Motile 4
70 Chlamydia psittaci Chlamydiaceae 24.00 NonEndemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 3
71 Clostridium tetani Clostridiaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 2
72 Enterococcus faecalis Enterococcaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 1
73 Streptobacillus moniliformis Leptotrichiaceae 36.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.500000 0.5 Motile 1
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
76 Acinetobacter baumannii Moraxellaceae 0.66 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Transmissable Noeffect 0.000000 0.0 Motile 1
In [29]:
print(bact_new.isnull().sum())

Pathogen                 0
Family                   0
GT                       0
Endemic                  0
Severity                 0
Severity_Scale           0
Route                    0
Tissue                   0
Sytemic                  0
Transmissibility         0
Aid                      0
Immune_killing           0
Immune_survival          0
Motility                 0
No.bacterial pathogen    0
dtype: int64
In [30]:
from sklearn.utils import resample
bact_new_upsampled= resample(bact_new,
             replace=True,
             n_samples=250,
             random_state=21)
In [31]:
bact_new_upsampled
Out[31]:
Pathogen Family GT Endemic Severity Severity_Scale Route Tissue Sytemic Transmissibility Aid Immune_killing Immune_survival Motility No.bacterial pathogen
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
5 Bacillus cereus d 0.30 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
49 Bartonella quintana Bartonellaceae 3.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Transmissable Noeffect 0.000000 0.0 Motile 3
36 Staphylococcus aureus Staphylococcaceae 0.40 NonEndemic Severe MoreSevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Motile 1
61 Francisella tularensis tularensis (Type A) Francisellaceae 3.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
73 Streptobacillus moniliformis Leptotrichiaceae 36.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.500000 0.5 Motile 1
64 Nocardia brasiliensis Nocardiaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 14
62 Francisella tularensis holarctica (Type B) Francisellaceae 3.00 NonEndemic Nonsevere LeastSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
49 Bartonella quintana Bartonellaceae 3.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Transmissable Noeffect 0.000000 0.0 Motile 3
60 Mycobacterium leprae Mycobacteriaceae 240.00 NonEndemic Severe MoreSevere Inahalation Respiratory Systemic Transmissable Noeffect 0.000000 1.0 Motile 4
21 Legionella pneumophila Legionellaceae 3.30 NonEndemic Severe Mostsevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
42 Vibrio vulnificus Vibrionaceae 0.16 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 0.0 Nonmotile 3
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
19 Haemophilus ducreyi Pasteurellaceae 1.80 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 2
71 Clostridium tetani Clostridiaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 2
51 Burkholderia pseudomallei Burkholderiaceae 1.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 2
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
49 Bartonella quintana Bartonellaceae 3.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Transmissable Noeffect 0.000000 0.0 Motile 3
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 0.0 Nonmotile 2
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
36 Staphylococcus aureus Staphylococcaceae 0.40 NonEndemic Severe MoreSevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Motile 1
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
13 Corynebacterium diphtheriae Corynebacteriaceae 2.00 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.500000 0.0 Motile 1
16 E coli EIEC Enterobacteriaceae 0.40 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
7 Bordatella pertussis Alcaligenaceae 3.80 Endemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Transmissable Helps 1.000000 1.0 Motile 1
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.666667 1.0 Motile 4
10 Brucella suis Brucellaceae 2.00 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
1 Aeromonas hydrophila Aeromonadaceae 0.35 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Help 0.000000 0.0 Nonmotile 1
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
70 Chlamydia psittaci Chlamydiaceae 24.00 NonEndemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 3
58 Ehrlichia chaffeensis Anaplasmataceae 19.00 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
5 Bacillus cereus d 0.30 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 Endemic Severe Mostsevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Nonmotile 14
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 Endemic Severe Mostsevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Nonmotile 14
26 Orientia tsutsugamushi Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
33 Shigella dysenteriae Enterobacteriaceae 0.67 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
33 Shigella dysenteriae Enterobacteriaceae 0.67 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
64 Nocardia brasiliensis Nocardiaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
26 Orientia tsutsugamushi Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 0.0 Nonmotile 2
67 Fusobacterium nucleatum Fusobacteriaceae 0.72 Endemic Nonsevere Mostsevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Motile 1
72 Enterococcus faecalis Enterococcaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 1
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
9 Brucella melitensis Brucellaceae 2.00 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 1.0 Motile 4
59 Klebsiella granulomatis Enterobacteriaceae 129.50 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 14
51 Burkholderia pseudomallei Burkholderiaceae 1.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 2
25 Neisseria meningitidis Neisseriaceae 0.72 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Noeffect 0.000000 0.0 Motile 2
26 Orientia tsutsugamushi Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
65 Erysipelothrix rhusiopathiae Erysiopelotrichaceae 13.50 NonEndemic Nonsevere MoreSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
26 Orientia tsutsugamushi Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
48 Bartonella bacilliformis Bartonellaceae 24.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.000000 1.0 Nonmotile 3
40 Vibrio cholerae Vibrionaceae 0.20 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 3
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
44 Yersinia pestis Enterobacteriaceae 1.25 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Hinder 1.000000 1.0 Motile 14
19 Haemophilus ducreyi Pasteurellaceae 1.80 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 2
40 Vibrio cholerae Vibrionaceae 0.20 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 3
5 Bacillus cereus d 0.30 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
35 Shigella sonnei Enterobacteriaceae 0.50 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
51 Burkholderia pseudomallei Burkholderiaceae 1.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 2
58 Ehrlichia chaffeensis Anaplasmataceae 19.00 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
17 E coli EPEC Enterobacteriaceae 0.40 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 14
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
52 Burkholderia mallei Burkholderiaceae 0.75 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
28 Rickettsia conorii (SFG) Rickettsiaceae 4.10 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.333333 1.0 Motile 4
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
33 Shigella dysenteriae Enterobacteriaceae 0.67 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
32 Salmonella enterica s. Typhimurium Enterobacteriaceae 0.40 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
67 Fusobacterium nucleatum Fusobacteriaceae 0.72 Endemic Nonsevere Mostsevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Motile 1
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
68 Haemophilus influenzae Type B Pasteurellaceae 0.50 Endemic Nonsevere MoreSevere Inahalation Respiratory Systemic Transmissable Helps 0.000000 0.0 Motile 2
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
66 Mycobacterium marinum Mycobacteriaceae 24.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 3
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
12 Clostridium perfringens Clostridiaceae 0.20 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 2
12 Clostridium perfringens Clostridiaceae 0.20 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 2
56 Chlamydia pneumoniae Chlamydiaceae 24.00 Endemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.000000 1.0 Motile 3
37 Streptococcus pneumoniae Streptococcaceae 0.50 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.000000 0.0 Motile 2
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
30 Rickettsia rickettsii (SFG) Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 1.000000 1.0 Motile 4
4 Bacillus anthracis Bacillaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 1.000000 0.0 Motile 1
39 Treponema pallidum Spirochaetaceae 33.00 Endemic Severe Mostsevere Sexual Genital Systemic Transmissable Helps 0.000000 0.5 Nonmotile 3
47 Bartonella henselae Bartonellaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 3
25 Neisseria meningitidis Neisseriaceae 0.72 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Noeffect 0.000000 0.0 Motile 2
66 Mycobacterium marinum Mycobacteriaceae 24.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
42 Vibrio vulnificus Vibrionaceae 0.16 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 0.0 Nonmotile 3
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
62 Francisella tularensis holarctica (Type B) Francisellaceae 3.00 NonEndemic Nonsevere LeastSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
26 Orientia tsutsugamushi Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
36 Staphylococcus aureus Staphylococcaceae 0.40 NonEndemic Severe MoreSevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Motile 1
11 Campylobacter jejuni Campylobacteraceae 1.50 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
69 Pasteurella multocida Brucellaceae 48.00 NonEndemic Nonsevere MoreSevere Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Motile 4
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.666667 1.0 Motile 4
17 E coli EPEC Enterobacteriaceae 0.40 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 14
35 Shigella sonnei Enterobacteriaceae 0.50 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
42 Vibrio vulnificus Vibrionaceae 0.16 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 0.0 Nonmotile 3
1 Aeromonas hydrophila Aeromonadaceae 0.35 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Help 0.000000 0.0 Nonmotile 1
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 Endemic Severe Mostsevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Nonmotile 14
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
66 Mycobacterium marinum Mycobacteriaceae 24.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
37 Streptococcus pneumoniae Streptococcaceae 0.50 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.000000 0.0 Motile 2
62 Francisella tularensis holarctica (Type B) Francisellaceae 3.00 NonEndemic Nonsevere LeastSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 0.0 Nonmotile 2
1 Aeromonas hydrophila Aeromonadaceae 0.35 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Help 0.000000 0.0 Nonmotile 1
4 Bacillus anthracis Bacillaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 1.000000 0.0 Motile 1
8 Brucella abortus Brucellaceae 2.00 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
33 Shigella dysenteriae Enterobacteriaceae 0.67 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 0.0 Nonmotile 2
11 Campylobacter jejuni Campylobacteraceae 1.50 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
24 Neisseria gonorrhoeae Neisseriaceae 0.58 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 2
44 Yersinia pestis Enterobacteriaceae 1.25 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Hinder 1.000000 1.0 Motile 14
40 Vibrio cholerae Vibrionaceae 0.20 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 3
13 Corynebacterium diphtheriae Corynebacteriaceae 2.00 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.500000 0.0 Motile 1
36 Staphylococcus aureus Staphylococcaceae 0.40 NonEndemic Severe MoreSevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Motile 1
32 Salmonella enterica s. Typhimurium Enterobacteriaceae 0.40 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
49 Bartonella quintana Bartonellaceae 3.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Transmissable Noeffect 0.000000 0.0 Motile 3
19 Haemophilus ducreyi Pasteurellaceae 1.80 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 2
15 E coli EHEC Enterobacteriaceae 0.33 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Systemic Transmissable Helps 1.000000 1.0 Nonmotile 14
4 Bacillus anthracis Bacillaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 1.000000 0.0 Motile 1
27 Plesiomonas shigelloides Enterobacteriaceae 0.43 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 14
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 14
13 Corynebacterium diphtheriae Corynebacteriaceae 2.00 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Helps 0.500000 0.0 Motile 1
66 Mycobacterium marinum Mycobacteriaceae 24.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
70 Chlamydia psittaci Chlamydiaceae 24.00 NonEndemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 3
55 Borrelia burgdorferi Spirochaetaceae 4.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 3
4 Bacillus anthracis Bacillaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 1.000000 0.0 Motile 1
23 Mycobacterium tuberculosis Mycobacteriaceae 19.00 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Helps 1.000000 1.0 Motile 4
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
12 Clostridium perfringens Clostridiaceae 0.20 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 2
20 Helicobacter pylori Helicobacteraceae 2.40 Endemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
40 Vibrio cholerae Vibrionaceae 0.20 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 3
12 Clostridium perfringens Clostridiaceae 0.20 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 2
1 Aeromonas hydrophila Aeromonadaceae 0.35 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Help 0.000000 0.0 Nonmotile 1
70 Chlamydia psittaci Chlamydiaceae 24.00 NonEndemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 3
44 Yersinia pestis Enterobacteriaceae 1.25 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Hinder 1.000000 1.0 Motile 14
66 Mycobacterium marinum Mycobacteriaceae 24.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
14 Coxiella burnetii Coxiellaceae 8.00 NonEndemic Nonsevere Severe Inahalation Respiratory Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
43 Yersinia enterocolitica Enterobacteriaceae 0.55 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 14
24 Neisseria gonorrhoeae Neisseriaceae 0.58 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 2
3 Arcobacter butzleri Arcobacteraceae 0.66 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
76 Acinetobacter baumannii Moraxellaceae 0.66 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Transmissable Noeffect 0.000000 0.0 Motile 1
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.666667 1.0 Motile 4
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 3
8 Brucella abortus Brucellaceae 2.00 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
46 Leptospira interrogans Spirochaetaceae 9.00 NonEndemic Severe Mostsevere Direct Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
11 Campylobacter jejuni Campylobacteraceae 1.50 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
32 Salmonella enterica s. Typhimurium Enterobacteriaceae 0.40 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
23 Mycobacterium tuberculosis Mycobacteriaceae 19.00 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Helps 1.000000 1.0 Motile 4
65 Erysipelothrix rhusiopathiae Erysiopelotrichaceae 13.50 NonEndemic Nonsevere MoreSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
18 E coli ETEC Enterobacteriaceae 0.33 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 14
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
70 Chlamydia psittaci Chlamydiaceae 24.00 NonEndemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 3
55 Borrelia burgdorferi Spirochaetaceae 4.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
22 Listeria monocytogenes Listeriaceae 1.00 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
75 Stenotrophomonas maltophilia Xanthomonadaceae 0.60 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
12 Clostridium perfringens Clostridiaceae 0.20 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 2
16 E coli EIEC Enterobacteriaceae 0.40 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
40 Vibrio cholerae Vibrionaceae 0.20 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 3
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
33 Shigella dysenteriae Enterobacteriaceae 0.67 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
19 Haemophilus ducreyi Pasteurellaceae 1.80 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 2
68 Haemophilus influenzae Type B Pasteurellaceae 0.50 Endemic Nonsevere MoreSevere Inahalation Respiratory Systemic Transmissable Helps 0.000000 0.0 Motile 2
68 Haemophilus influenzae Type B Pasteurellaceae 0.50 Endemic Nonsevere MoreSevere Inahalation Respiratory Systemic Transmissable Helps 0.000000 0.0 Motile 2
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
63 Mycobacterium bovis Mycobacteriaceae 23.00 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
26 Orientia tsutsugamushi Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 4
55 Borrelia burgdorferi Spirochaetaceae 4.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
47 Bartonella henselae Bartonellaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 3
27 Plesiomonas shigelloides Enterobacteriaceae 0.43 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 14
67 Fusobacterium nucleatum Fusobacteriaceae 0.72 Endemic Nonsevere Mostsevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Motile 1
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
76 Acinetobacter baumannii Moraxellaceae 0.66 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Transmissable Noeffect 0.000000 0.0 Motile 1
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 Endemic Severe Mostsevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Nonmotile 14
76 Acinetobacter baumannii Moraxellaceae 0.66 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Transmissable Noeffect 0.000000 0.0 Motile 1
55 Borrelia burgdorferi Spirochaetaceae 4.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
39 Treponema pallidum Spirochaetaceae 33.00 Endemic Severe Mostsevere Sexual Genital Systemic Transmissable Helps 0.000000 0.5 Nonmotile 3
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
76 Acinetobacter baumannii Moraxellaceae 0.66 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Transmissable Noeffect 0.000000 0.0 Motile 1
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
72 Enterococcus faecalis Enterococcaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 1
21 Legionella pneumophila Legionellaceae 3.30 NonEndemic Severe Mostsevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
4 Bacillus anthracis Bacillaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 1.000000 0.0 Motile 1
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
41 Vibrio parahaemolyticus Vibrionaceae 0.20 NonEndemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
65 Erysipelothrix rhusiopathiae Erysiopelotrichaceae 13.50 NonEndemic Nonsevere MoreSevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
38 Streptococcus pyogenes (group A) Streptococcaceae 0.40 Endemic Severe Mostsevere Inahalation Respiratory Nonsystemic Transmissable Noeffect 1.000000 1.0 Motile 2
55 Borrelia burgdorferi Spirochaetaceae 4.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
61 Francisella tularensis tularensis (Type A) Francisellaceae 3.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
4 Bacillus anthracis Bacillaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 1.000000 0.0 Motile 1
29 Rickettsia prowazekii (TG) Rickettsiaceae 10.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.666667 1.0 Motile 4
74 Pseudomonas aeruginosa Pseudomonadaceae 7.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
48 Bartonella bacilliformis Bartonellaceae 24.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Transmissable Noeffect 0.000000 1.0 Nonmotile 3
18 E coli ETEC Enterobacteriaceae 0.33 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 14
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 14
71 Clostridium tetani Clostridiaceae 0.50 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 2
2 Anaplasma phagocytophilum Anaplasmataceae 7.00 NonEndemic Nonsevere Severe Vector Bloodstream Systemic Nontransmissable Hinders 0.000000 1.0 Motile 1
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 3
31 Salmonella enterica s. typhi Enterobacteriaceae 0.40 Endemic Severe Mostsevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Nonmotile 14
39 Treponema pallidum Spirochaetaceae 33.00 Endemic Severe Mostsevere Sexual Genital Systemic Transmissable Helps 0.000000 0.5 Nonmotile 3
47 Bartonella henselae Bartonellaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 3
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 3
23 Mycobacterium tuberculosis Mycobacteriaceae 19.00 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Helps 1.000000 1.0 Motile 4
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 0.0 Nonmotile 2
72 Enterococcus faecalis Enterococcaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 1
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 14
19 Haemophilus ducreyi Pasteurellaceae 1.80 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 2
61 Francisella tularensis tularensis (Type A) Francisellaceae 3.00 NonEndemic Severe Mostsevere Direct Cutaneous Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 2
58 Ehrlichia chaffeensis Anaplasmataceae 19.00 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
30 Rickettsia rickettsii (SFG) Rickettsiaceae 9.00 NonEndemic Severe Mostsevere Vector Bloodstream Systemic Nontransmissable Noeffect 1.000000 1.0 Motile 4
27 Plesiomonas shigelloides Enterobacteriaceae 0.43 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Nonmotile 14
22 Listeria monocytogenes Listeriaceae 1.00 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
59 Klebsiella granulomatis Enterobacteriaceae 129.50 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 14
24 Neisseria gonorrhoeae Neisseriaceae 0.58 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 2
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 0.0 Nonmotile 2
35 Shigella sonnei Enterobacteriaceae 0.50 Endemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
20 Helicobacter pylori Helicobacteraceae 2.40 Endemic Nonsevere MoreSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
70 Chlamydia psittaci Chlamydiaceae 24.00 NonEndemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 3
6 Bacteroides fragilis Bacteroidaceae 0.67 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Systemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
34 Shigella flexneri Enterobacteriaceae 0.68 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Motile 14
33 Shigella dysenteriae Enterobacteriaceae 0.67 Endemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
16 E coli EIEC Enterobacteriaceae 0.40 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 1.000000 1.0 Nonmotile 14
50 Chlamydia trachomati, Serovar B->D Chlamydiaceae 24.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 1.0 Motile 3
55 Borrelia burgdorferi Spirochaetaceae 4.00 NonEndemic Nonsevere LeastSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 3
28 Rickettsia conorii (SFG) Rickettsiaceae 4.10 NonEndemic Nonsevere MoreSevere Vector Bloodstream Systemic Nontransmissable Noeffect 0.333333 1.0 Motile 4
36 Staphylococcus aureus Staphylococcaceae 0.40 NonEndemic Severe MoreSevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Motile 1
36 Staphylococcus aureus Staphylococcaceae 0.40 NonEndemic Severe MoreSevere Ingestion Gastrointestinal Systemic Transmissable Noeffect 1.000000 1.0 Motile 1
5 Bacillus cereus d 0.30 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
11 Campylobacter jejuni Campylobacteraceae 1.50 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Nonmotile 1
25 Neisseria meningitidis Neisseriaceae 0.72 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Noeffect 0.000000 0.0 Motile 2
25 Neisseria meningitidis Neisseriaceae 0.72 Endemic Severe Mostsevere Inahalation Respiratory Systemic Transmissable Noeffect 0.000000 0.0 Motile 2
64 Nocardia brasiliensis Nocardiaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
57 Clostridium difficile Peptostreptococcaceae 0.50 NonEndemic Severe Mostsevere Ingestion Gastrointestinal Nonsystemic Transmissable Helps 0.000000 0.0 Nonmotile 1
3 Arcobacter butzleri Arcobacteraceae 0.66 NonEndemic Nonsevere LeastSevere Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 0.000000 0.0 Nonmotile 1
7 Bordatella pertussis Alcaligenaceae 3.80 Endemic Nonsevere MoreSevere Inahalation Respiratory Nonsystemic Transmissable Helps 1.000000 1.0 Motile 1
54 Mycoplasma genitalium Mycoplasmataceae 12.00 Endemic Nonsevere LeastSevere Sexual Genital Nonsystemic Transmissable Hinders 0.000000 0.0 Nonmotile 2
64 Nocardia brasiliensis Nocardiaceae 3.00 NonEndemic Nonsevere Severe Direct Cutaneous Nonsystemic Nontransmissable Noeffect 0.000000 1.0 Motile 1
45 Yersinia pseudotuberculosis Enterobacteriaceae 0.50 NonEndemic Nonsevere Severe Ingestion Gastrointestinal Nonsystemic Nontransmissable Noeffect 1.000000 1.0 Motile 14
In [32]:
#split dataset in features and target variable
feature_cols = ['Family', 'Endemic', 'Sytemic', 'Route','Tissue', 'Transmissibility','Immune_survival','Immune_killing']
X = bact_new_upsampled[feature_cols] # Features
y = bact_new_upsampled.Severity # Target variable
In [33]:
X_encoded = pd.get_dummies(X)
X_encoded
Out[33]:
Immune_survival Immune_killing Family_Aeromonadaceae Family_Alcaligenaceae Family_Anaplasmataceae Family_Anaplasmataceae Family_Arcobacteraceae Family_Bacillaceae Family_Bacteroidaceae Family_Bartonellaceae Family_Brucellaceae Family_Burkholderiaceae Family_Campylobacteraceae Family_Chlamydiaceae Family_Clostridiaceae Family_Corynebacteriaceae Family_Coxiellaceae Family_Enterobacteriaceae Family_Enterococcaceae Family_Erysiopelotrichaceae Family_Francisellaceae Family_Fusobacteriaceae Family_Helicobacteraceae Family_Legionellaceae Family_Leptotrichiaceae Family_Listeriaceae Family_Moraxellaceae Family_Mycobacteriaceae Family_Mycoplasmataceae Family_Neisseriaceae Family_Nocardiaceae Family_Pasteurellaceae Family_Peptostreptococcaceae Family_Pseudomonadaceae Family_Rickettsiaceae Family_Spirochaetaceae Family_Staphylococcaceae Family_Streptococcaceae Family_Vibrionaceae Family_Xanthomonadaceae Family_d Endemic_Endemic Endemic_NonEndemic Sytemic_Nonsystemic Sytemic_Systemic Route_Direct Route_Direct Route_Inahalation Route_Ingestion Route_Sexual Route_Vector Tissue_Bloodstream Tissue_Bloodstream Tissue_Cutaneous Tissue_Gastrointestinal Tissue_Genital Tissue_Respiratory Transmissibility_Nontransmissable Transmissibility_Transmissable
74 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
5 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
49 0.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
36 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
61 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
75 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
73 0.5 0.500000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0
64 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
45 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
62 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
49 0.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
60 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
21 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
42 0.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
19 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
71 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
51 1.0 0.000000 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
49 0.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
36 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
13 0.0 0.500000 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1
16 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
7 1.0 1.000000 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1
29 1.0 0.666667 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
10 1.0 0.000000 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
1 0.0 0.000000 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
70 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0
58 1.0 0.000000 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
5 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
31 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
31 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
26 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
33 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
33 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
64 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
26 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
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74 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
33 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
19 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
68 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
68 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
74 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
63 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
26 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
55 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
47 1.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0
27 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
67 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
2 1.0 0.000000 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
76 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 1
31 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
76 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 1
55 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 0 1 0
39 0.5 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
76 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 0 1
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
2 1.0 0.000000 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
72 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
21 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0
4 0.0 1.000000 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
41 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
65 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
38 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1
55 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 0 1 0
61 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
4 0.0 1.000000 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
29 1.0 0.666667 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
74 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
48 1.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
18 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
45 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
71 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
2 1.0 0.000000 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
50 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
31 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
39 0.5 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1
47 1.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0
50 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
23 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
72 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
45 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
19 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
61 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
58 1.0 0.000000 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
30 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
27 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
22 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
59 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
24 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
35 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
20 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
70 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
33 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
16 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
50 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
55 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 0 1 0
28 1.0 0.333333 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
36 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
36 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
5 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
11 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
25 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
25 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
64 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
3 0.0 0.000000 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
7 1.0 1.000000 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
64 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
45 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
In [34]:
from sklearn.preprocessing import LabelEncoder 
encoder = LabelEncoder() 
# apply on df 
y_encoded1 = encoder.fit_transform(y)
y_encoded1
Out[34]:
array([0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0,
       0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 0,
       0, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0,
       1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1,
       0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0,
       0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0,
       0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0,
       1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1,
       0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0,
       1, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1,
       0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1,
       1, 0, 1, 0, 0, 0, 0, 0])
In [35]:
from sklearn.model_selection import train_test_split
# Split dataset into training set and test set
X_train, X_test, y_train, y_test = train_test_split(X_encoded, y_encoded1, test_size=0.33,random_state=21)
In [36]:
from sklearn import svm
SV1 = svm.SVC(probability=True)


# Train Decision Tree Classifer
SV1.fit(X_train, y_train)
Out[36]:
SVC(probability=True)
In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook.
On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.
SVC(probability=True)
In [37]:
pred_y1_sv = SV1.predict(X_test)


pred_y1 = SV1.predict_proba(X_test)[:,1]

# auc scores
from sklearn.metrics import roc_auc_score,classification_report,confusion_matrix
auc_score1 = roc_auc_score(y_test, pred_y1_sv)
auc_score1
Out[37]:
0.8826593137254902
In [38]:
cr1 = classification_report(y_test, pred_y1_sv)
print('cr1:',cr1)

cr1:               precision    recall  f1-score   support

           0       0.90      0.92      0.91        51
           1       0.87      0.84      0.86        32

    accuracy                           0.89        83
   macro avg       0.89      0.88      0.88        83
weighted avg       0.89      0.89      0.89        83
In [39]:
cm1 = confusion_matrix(y_test, pred_y1_sv)

recall1 = np.diag(cm1) / np.sum(cm1, axis = 1)
precision1 = np.diag(cm1) / np.sum(cm1, axis = 0)
print('cm1:',cm1,
'precision1:',precision1,
'recall1:', recall1)

cm1: [[47  4]
 [ 5 27]] precision1: [0.90384615 0.87096774] recall1: [0.92156863 0.84375   ]
In [40]:
from sklearn.ensemble import RandomForestClassifier
RF1 = RandomForestClassifier()
RF1.fit(X_train, y_train)

pred_y2_rf = RF1.predict(X_test)
#Predict the response for test dataset
pred_y2 = RF1.predict_proba(X_test)[:,1]
# auc scores
from sklearn.metrics import roc_auc_score
auc_score2 = roc_auc_score(y_test, pred_y2)
auc_score2
Out[40]:
0.9846813725490196
In [41]:
cr2 = classification_report(y_test, pred_y2_rf)
print('cr2:',cr2)

cr2:               precision    recall  f1-score   support

           0       0.92      0.96      0.94        51
           1       0.93      0.88      0.90        32

    accuracy                           0.93        83
   macro avg       0.93      0.92      0.92        83
weighted avg       0.93      0.93      0.93        83
In [42]:
cm2 = confusion_matrix(y_test, pred_y2_rf)

recall2 = np.diag(cm2) / np.sum(cm2, axis = 1)
precision2 = np.diag(cm2) / np.sum(cm2, axis = 0)
print('cm2:',cm2,
'precision2:',precision2,
'recall2:', recall2)

cm2: [[49  2]
 [ 4 28]] precision2: [0.9245283  0.93333333] recall2: [0.96078431 0.875     ]
In [43]:
from sklearn.linear_model import LogisticRegression
LR1= LogisticRegression()
LR1.fit(X_train,y_train)
pred_y3_lr = LR1.predict(X_test)
#Predict the response for test dataset
pred_y3 = LR1.predict_proba(X_test)[:,1]
# auc scores
from sklearn.metrics import roc_auc_score
auc_score3 = roc_auc_score(y_test, pred_y3)
auc_score3
Out[43]:
0.9460784313725489
In [44]:
cr3 = classification_report(y_test, pred_y3_lr)
print('cr3:',cr3)

cr3:               precision    recall  f1-score   support

           0       0.88      0.90      0.89        51
           1       0.84      0.81      0.83        32

    accuracy                           0.87        83
   macro avg       0.86      0.86      0.86        83
weighted avg       0.87      0.87      0.87        83
In [45]:
cm3 = confusion_matrix(y_test, pred_y3_lr)

recall3 = np.diag(cm3) / np.sum(cm3, axis = 1)
precision3 = np.diag(cm3) / np.sum(cm3, axis = 0)
print('cm3:',cm3,
'precision3:',precision3,
'recall3:', recall3)

cm3: [[46  5]
 [ 6 26]] precision3: [0.88461538 0.83870968] recall3: [0.90196078 0.8125    ]
In [46]:
from sklearn.ensemble import GradientBoostingClassifier
GB1 = GradientBoostingClassifier()
GB1.fit(X_train,y_train)
pred_y4_gb = GB1.predict(X_test)
#Predict the response for test dataset
pred_y4 = GB1.predict_proba(X_test)[:,1]
# auc scores
from sklearn.metrics import roc_auc_score
auc_score4 = roc_auc_score(y_test, pred_y4)
auc_score4
Out[46]:
0.9712009803921569
In [47]:
cr4 = classification_report(y_test, pred_y4_gb)
print('cr4:',cr4)

cr4:               precision    recall  f1-score   support

           0       0.91      0.96      0.93        51
           1       0.93      0.84      0.89        32

    accuracy                           0.92        83
   macro avg       0.92      0.90      0.91        83
weighted avg       0.92      0.92      0.91        83
In [48]:
cm4 = confusion_matrix(y_test, pred_y4_gb)

recall4 = np.diag(cm4) / np.sum(cm4, axis = 1)
precision4 = np.diag(cm4) / np.sum(cm4, axis = 0)
print('cm4:',cm4,
'precision4:',precision4,
'recall4:', recall4)

cm4: [[49  2]
 [ 5 27]] precision4: [0.90740741 0.93103448] recall4: [0.96078431 0.84375   ]
In [49]:
from sklearn import model_selection
# prepare models
models = []
models.append(('SV1', svm.SVC()))
models.append(('RF1', RandomForestClassifier()))
models.append(('LR1', LogisticRegression()))
models.append(('GB1', GradientBoostingClassifier()))

# evaluate each model in turn
results = []
names = []
scoring = 'accuracy'
for name, model in models:
    kfold = model_selection.KFold(n_splits=10)
    cv_results = model_selection.cross_val_score(model, X_test, y_test, cv=kfold, scoring=scoring)
    results.append(cv_results)
    names.append(name)
    msg = "%s: %f (%f)" % (name, cv_results.mean(), cv_results.std())
    print(msg)
# boxplot algorithm comparison
fig = plt.figure()
fig.suptitle('Algorithm Comparison')
ax = fig.add_subplot(111)
plt.boxplot(results)
ax.set_xticklabels(names)
plt.show()

SV1: 0.758333 (0.123009)
RF1: 0.818056 (0.115612)
LR1: 0.783333 (0.088541)
GB1: 0.830556 (0.139000)
In [50]:
from matplotlib import pyplot
from sklearn import metrics
# calculate roc curves
sv_fpr, sv_tpr, _ = metrics.roc_curve(y_test, pred_y1)
rf_fpr, rf_tpr, _ = metrics.roc_curve(y_test, pred_y2)
lr_fpr, lr_tpr, _ = metrics.roc_curve(y_test, pred_y3)
gb_fpr, gb_tpr, _ = metrics.roc_curve(y_test, pred_y4)
# plot the roc curve for the model
pyplot.plot(sv_fpr, sv_tpr, linestyle='--', label='SVM')
pyplot.plot(rf_fpr, rf_tpr, linestyle='--', label='Randomforest')
pyplot.plot(lr_fpr, lr_tpr, linestyle='--', label='Logisticreg')
pyplot.plot(gb_fpr, gb_tpr, linestyle='--', label='Gradientboost')
# axis labels
pyplot.xlabel('False Positive Rate')
pyplot.ylabel('True Positive Rate')
# show the legend
pyplot.legend()
# show the plot
pyplot.show()
In [51]:
feature_scores = pd.Series(RF1.feature_importances_, index=X_train.columns).sort_values(ascending=False)

feature_scores
Out[51]:
Immune_killing                       0.108458
Sytemic_Nonsystemic                  0.066280
Family_Peptostreptococcaceae         0.049520
Sytemic_Systemic                     0.045685
Family_Rickettsiaceae                0.043572
Immune_survival                      0.040510
Family_Bacteroidaceae                0.036057
Transmissibility_Transmissable       0.034400
Transmissibility_Nontransmissable    0.034318
Endemic_Endemic                      0.030348
Endemic_NonEndemic                   0.025807
Family_Enterobacteriaceae            0.024874
Route_Sexual                         0.022787
Tissue_Gastrointestinal              0.021328
Tissue_Genital                       0.020390
Family_Brucellaceae                  0.020311
Family_Staphylococcaceae             0.019687
Family_Anaplasmataceae               0.019598
Family_Bacillaceae                   0.019513
Family_Burkholderiaceae              0.018446
Route_Ingestion                      0.017520
Family_Vibrionaceae                  0.016156
Family_Clostridiaceae                0.015865
Route_Direct                         0.014814
Tissue_Bloodstream                   0.014622
Family_Bartonellaceae                0.014322
Route_Inahalation                    0.014301
Family_Pseudomonadaceae              0.014223
Tissue_Respiratory                   0.013537
Family_Pasteurellaceae               0.013234
Tissue_Cutaneous                     0.012302
Route_Vector                         0.012218
Family_Chlamydiaceae                 0.011860
Family_Francisellaceae               0.009855
Family_Neisseriaceae                 0.009658
Tissue_Bloodstream                   0.008313
Family_Legionellaceae                0.008119
Family_Xanthomonadaceae              0.007568
Family_Streptococcaceae              0.007168
Family_Erysiopelotrichaceae          0.007149
Family_Anaplasmataceae               0.006927
Family_Alcaligenaceae                0.006891
Family_Moraxellaceae                 0.006858
Family_Spirochaetaceae               0.006622
Family_Corynebacteriaceae            0.006513
Family_Mycobacteriaceae              0.004317
Route_Direct                         0.003901
Family_Listeriaceae                  0.003728
Family_Leptotrichiaceae              0.002475
Family_Coxiellaceae                  0.001459
Family_Mycoplasmataceae              0.001257
Family_Enterococcaceae               0.001228
Family_Campylobacteraceae            0.000669
Family_Arcobacteraceae               0.000653
Family_Nocardiaceae                  0.000527
Family_Fusobacteriaceae              0.000485
Family_Aeromonadaceae                0.000435
Family_d                             0.000364
Family_Helicobacteraceae             0.000000
dtype: float64
In [52]:
import seaborn as sns
f, ax = plt.subplots(figsize=(20, 20))
ax = sns.barplot(x=feature_scores, y=feature_scores.index, data=bact_new)
ax.set_title("Visualize feature scores of the features")
ax.set_yticklabels(feature_scores.index)
ax.set_xlabel("Feature importance score")
ax.set_ylabel("Features")
fig.tight_layout()
plt.show()
In [53]:
#split dataset in features and target variable
feature_cols2 = [ 'Family','Endemic', 'Sytemic', 'Route','Tissue', 'Transmissibility','Immune_survival','Immune_killing']
X2 = bact_new_upsampled[feature_cols2] # Features
y2 = bact_new_upsampled.Severity_Scale # Target variable
In [54]:
from sklearn.preprocessing import LabelEncoder 
encoder = LabelEncoder() 
# apply on df 
y_encoded2 = encoder.fit_transform(y2)
y_encoded2
Out[54]:
array([3, 2, 0, 0, 1, 2, 3, 2, 3, 3, 0, 0, 1, 2, 2, 2, 2, 0, 2, 2, 2, 0,
       0, 2, 1, 2, 2, 0, 1, 2, 3, 1, 2, 1, 1, 0, 2, 2, 2, 2, 2, 3, 2, 0,
       2, 3, 2, 1, 0, 2, 2, 2, 1, 2, 2, 3, 2, 2, 0, 3, 0, 0, 2, 1, 3, 3,
       2, 3, 1, 2, 2, 0, 2, 3, 1, 3, 3, 2, 0, 2, 0, 0, 1, 2, 3, 2, 2, 2,
       3, 2, 3, 2, 3, 0, 2, 1, 0, 3, 1, 2, 3, 0, 2, 1, 2, 2, 3, 3, 2, 0,
       0, 1, 2, 0, 2, 0, 0, 0, 2, 3, 2, 1, 0, 0, 0, 1, 2, 3, 3, 2, 3, 1,
       0, 3, 0, 2, 2, 2, 0, 1, 3, 0, 1, 1, 2, 3, 3, 3, 0, 0, 3, 2, 0, 0,
       2, 0, 0, 2, 1, 3, 3, 1, 0, 2, 3, 0, 0, 3, 3, 2, 0, 1, 1, 3, 0, 2,
       0, 2, 3, 3, 2, 3, 3, 2, 3, 0, 2, 2, 3, 2, 3, 2, 3, 2, 2, 2, 1, 1,
       2, 0, 2, 2, 2, 3, 2, 3, 3, 2, 3, 0, 2, 2, 3, 0, 2, 0, 3, 3, 0, 2,
       1, 2, 3, 2, 0, 0, 0, 0, 1, 1, 2, 2, 2, 0, 0, 0, 1, 1, 1, 0, 0, 2,
       2, 3, 2, 0, 1, 0, 3, 3])
In [55]:
X2_encoded = pd.get_dummies(X2)
X2_encoded
Out[55]:
Immune_survival Immune_killing Family_Aeromonadaceae Family_Alcaligenaceae Family_Anaplasmataceae Family_Anaplasmataceae Family_Arcobacteraceae Family_Bacillaceae Family_Bacteroidaceae Family_Bartonellaceae Family_Brucellaceae Family_Burkholderiaceae Family_Campylobacteraceae Family_Chlamydiaceae Family_Clostridiaceae Family_Corynebacteriaceae Family_Coxiellaceae Family_Enterobacteriaceae Family_Enterococcaceae Family_Erysiopelotrichaceae Family_Francisellaceae Family_Fusobacteriaceae Family_Helicobacteraceae Family_Legionellaceae Family_Leptotrichiaceae Family_Listeriaceae Family_Moraxellaceae Family_Mycobacteriaceae Family_Mycoplasmataceae Family_Neisseriaceae Family_Nocardiaceae Family_Pasteurellaceae Family_Peptostreptococcaceae Family_Pseudomonadaceae Family_Rickettsiaceae Family_Spirochaetaceae Family_Staphylococcaceae Family_Streptococcaceae Family_Vibrionaceae Family_Xanthomonadaceae Family_d Endemic_Endemic Endemic_NonEndemic Sytemic_Nonsystemic Sytemic_Systemic Route_Direct Route_Direct Route_Inahalation Route_Ingestion Route_Sexual Route_Vector Tissue_Bloodstream Tissue_Bloodstream Tissue_Cutaneous Tissue_Gastrointestinal Tissue_Genital Tissue_Respiratory Transmissibility_Nontransmissable Transmissibility_Transmissable
74 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
5 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
49 0.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
36 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
61 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
75 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
73 0.5 0.500000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0
64 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
45 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
62 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
49 0.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
60 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
21 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
42 0.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
19 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
71 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
51 1.0 0.000000 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
49 0.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
36 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
13 0.0 0.500000 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1
16 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
7 1.0 1.000000 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1
29 1.0 0.666667 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
10 1.0 0.000000 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
1 0.0 0.000000 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
70 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0
58 1.0 0.000000 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
5 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
31 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
31 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
26 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
33 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
33 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
64 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
26 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
67 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
72 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
9 1.0 1.000000 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
59 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
51 1.0 0.000000 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
25 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
26 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
65 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
26 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
48 1.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
40 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
44 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
19 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
40 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
5 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
35 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
51 1.0 0.000000 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
58 1.0 0.000000 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
17 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
2 1.0 0.000000 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
52 1.0 0.000000 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
2 1.0 0.000000 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
28 1.0 0.333333 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
33 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
32 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
67 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
75 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
68 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
2 1.0 0.000000 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
66 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
50 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
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48 1.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 0 1
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2 1.0 0.000000 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
50 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
31 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
39 0.5 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1
47 1.0 0.000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0
50 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
23 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
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19 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
61 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0
58 1.0 0.000000 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
30 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
27 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
22 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
59 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
24 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
35 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
20 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
70 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 1 0
6 1.0 0.000000 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0
34 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
33 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
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55 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 0 1 0
28 1.0 0.333333 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 1 0 0 0 0 0 1 0
36 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
36 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 0 1
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11 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
25 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 0 0 0 1 0 1
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64 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
57 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1
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7 1.0 1.000000 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1
54 0.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1
64 1.0 0.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0
45 1.0 1.000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0
In [56]:
from sklearn.model_selection import train_test_split
# Split dataset into training set and test set
X_train2, X_test2, y_train2, y_test2 = train_test_split(X2_encoded, y2, test_size=0.33, random_state=21)
In [57]:
from sklearn import svm
SV2 = svm.SVC(probability=True)


# Train Decision Tree Classifer
SV2.fit(X_train2, y_train2)
Out[57]:
SVC(probability=True)
In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook.
On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.
SVC(probability=True)
In [58]:
pred_y1_sv1 = SV2.predict(X_test2)
#Predict the response for test dataset
y_pred_proba1=SV2.predict_proba(X_test2)

#roc_auc
auc_score_1= roc_auc_score(y_test2, y_pred_proba1,multi_class='ovr')
auc_score_1
Out[58]:
0.9502962342121183
In [59]:
cr5 = classification_report(y_test2, pred_y1_sv1)
print('cr5:',cr5)

cr5:               precision    recall  f1-score   support

 LeastSevere       0.83      0.79      0.81        19
  MoreSevere       1.00      0.17      0.29        12
  Mostsevere       0.72      0.91      0.81        32
      Severe       0.87      1.00      0.93        20

    accuracy                           0.80        83
   macro avg       0.86      0.72      0.71        83
weighted avg       0.82      0.80      0.76        83
In [60]:
cm5 = confusion_matrix(y_test2, pred_y1_sv1)

recall5 = np.diag(cm5) / np.sum(cm5)
precision5 = np.diag(cm5) / np.sum(cm5)
print('cm5:',cm5,
'precision5:',precision5,
'recall5:', recall5)

cm5: [[15  0  4  0]
 [ 0  2  7  3]
 [ 3  0 29  0]
 [ 0  0  0 20]] precision5: [0.18072289 0.02409639 0.34939759 0.24096386] recall5: [0.18072289 0.02409639 0.34939759 0.24096386]
In [61]:
RF2 = RandomForestClassifier()
RF2.fit(X_train2, y_train2)
pred_y2_rf1 = RF2.predict(X_test)
#Predict the response for test dataset
y_pred_proba2=RF2.predict_proba(X_test2)
#roc_auc
auc_score_2 = roc_auc_score(y_test2, y_pred_proba2,multi_class='ovr')
auc_score_2
Out[61]:
0.9838016018583119
In [62]:
cr6 = classification_report(y_test2, pred_y2_rf1)
print('cr6:',cr6)

cr6:               precision    recall  f1-score   support

 LeastSevere       0.77      0.89      0.83        19
  MoreSevere       1.00      0.75      0.86        12
  Mostsevere       0.88      0.88      0.88        32
      Severe       1.00      1.00      1.00        20

    accuracy                           0.89        83
   macro avg       0.91      0.88      0.89        83
weighted avg       0.90      0.89      0.89        83
In [63]:
cm6 = confusion_matrix(y_test2, pred_y2_rf1)

recall6 = np.diag(cm6) / np.sum(cm6)
precision6 = np.diag(cm6) / np.sum(cm6)
print('cm6:',cm6,
'precision6:',precision6,
'recall6:', recall6)

cm6: [[17  0  2  0]
 [ 1  9  2  0]
 [ 4  0 28  0]
 [ 0  0  0 20]] precision6: [0.20481928 0.10843373 0.3373494  0.24096386] recall6: [0.20481928 0.10843373 0.3373494  0.24096386]
In [64]:
from sklearn.linear_model import LogisticRegression
LR2= LogisticRegression()
LR2.fit(X_train2,y_train2)
pred_y3_lr1 = LR2.predict(X_test2)
#Predict the response for test dataset
y_pred_proba3=LR2.predict_proba(X_test2)
#roc_auc
auc_score_3 = roc_auc_score(y_test2, y_pred_proba3,multi_class='ovr')
auc_score_3
Out[64]:
0.9077039101871289
In [65]:
cr7 = classification_report(y_test2, pred_y3_lr1)
print('cr7:',cr7)

cr7:               precision    recall  f1-score   support

 LeastSevere       0.79      0.79      0.79        19
  MoreSevere       0.86      0.50      0.63        12
  Mostsevere       0.79      0.84      0.82        32
      Severe       0.87      1.00      0.93        20

    accuracy                           0.82        83
   macro avg       0.83      0.78      0.79        83
weighted avg       0.82      0.82      0.81        83
In [66]:
cm7 = confusion_matrix(y_test2, pred_y3_lr1)

recall7 = np.diag(cm7) / np.sum(cm7)
precision7 = np.diag(cm7) / np.sum(cm7)
print('cm7:',cm7,
'precision7:',precision7,
'recall7:', recall7)

cm7: [[15  0  4  0]
 [ 0  6  3  3]
 [ 4  1 27  0]
 [ 0  0  0 20]] precision7: [0.18072289 0.07228916 0.3253012  0.24096386] recall7: [0.18072289 0.07228916 0.3253012  0.24096386]
In [67]:
from sklearn.ensemble import GradientBoostingClassifier
GB2 = GradientBoostingClassifier()
GB2.fit(X_train2,y_train2)
pred_y4_gb1 = GB2.predict(X_test2)
#Predict the response for test dataset
y_pred_proba4 = GB2.predict_proba(X_test2)
# auc scores
from sklearn.metrics import roc_auc_score
auc_score_4 = roc_auc_score(y_test2,  y_pred_proba4,multi_class='ovr')
auc_score_4
Out[67]:
0.9530207636860032
In [68]:
cr8 = classification_report(y_test2, pred_y4_gb1)
print('cr8:',cr8)

cr8:               precision    recall  f1-score   support

 LeastSevere       0.81      0.89      0.85        19
  MoreSevere       1.00      0.75      0.86        12
  Mostsevere       0.88      0.88      0.88        32
      Severe       0.95      1.00      0.98        20

    accuracy                           0.89        83
   macro avg       0.91      0.88      0.89        83
weighted avg       0.90      0.89      0.89        83
In [69]:
cm8 = confusion_matrix(y_test2, pred_y4_gb1)

recall8 = np.diag(cm8) / np.sum(cm8)
precision8 = np.diag(cm8) / np.sum(cm8)
print('cm8:',cm8,
'precision8:',precision8,
'recall8:', recall8)

cm8: [[17  0  2  0]
 [ 0  9  2  1]
 [ 4  0 28  0]
 [ 0  0  0 20]] precision8: [0.20481928 0.10843373 0.3373494  0.24096386] recall8: [0.20481928 0.10843373 0.3373494  0.24096386]
In [70]:
from sklearn import model_selection
# prepare models
models = []
models.append(('SV2', svm.SVC()))
models.append(('RF2', RandomForestClassifier()))
models.append(('LR2', LogisticRegression()))
models.append(('GB2', GradientBoostingClassifier()))

# evaluate each model in turn
results = []
names = []
scoring = 'accuracy'
for name, model in models:
    kfold = model_selection.KFold(n_splits=10)
    cv_results = model_selection.cross_val_score(model, X_test2, y_test2, cv=kfold, scoring=scoring)
    results.append(cv_results)
    names.append(name)
    msg = "%s: %f (%f)" % (name, cv_results.mean(), cv_results.std())
    print(msg)
# boxplot algorithm comparison
fig = plt.figure()
fig.suptitle('Algorithm Comparison')
ax = fig.add_subplot(111)
plt.boxplot(results)
ax.set_xticklabels(names)
plt.show()

SV2: 0.661111 (0.104896)
RF2: 0.769444 (0.116402)
LR2: 0.709722 (0.079894)
GB2: 0.769444 (0.116402)
In [71]:
feature_scores = pd.Series(RF2.feature_importances_, index=X_train.columns).sort_values(ascending=False)

feature_scores
Out[71]:
Immune_killing                       0.070458
Immune_survival                      0.050312
Route_Sexual                         0.041622
Sytemic_Systemic                     0.037137
Family_Enterobacteriaceae            0.035627
Transmissibility_Transmissable       0.032418
Sytemic_Nonsystemic                  0.032241
Family_Anaplasmataceae               0.031592
Tissue_Genital                       0.029909
Endemic_Endemic                      0.029725
Endemic_NonEndemic                   0.028608
Family_Peptostreptococcaceae         0.027966
Transmissibility_Nontransmissable    0.027614
Tissue_Respiratory                   0.024711
Route_Ingestion                      0.024112
Family_Brucellaceae                  0.023955
Family_Staphylococcaceae             0.021438
Family_Rickettsiaceae                0.020525
Route_Inahalation                    0.020036
Family_Clostridiaceae                0.018503
Tissue_Cutaneous                     0.017923
Family_Chlamydiaceae                 0.017749
Family_Erysiopelotrichaceae          0.017565
Tissue_Gastrointestinal              0.017322
Family_Bacteroidaceae                0.017123
Tissue_Bloodstream                   0.015716
Family_Francisellaceae               0.015146
Route_Vector                         0.014902
Family_Aeromonadaceae                0.014646
Family_Spirochaetaceae               0.013629
Tissue_Bloodstream                   0.013200
Family_Pseudomonadaceae              0.013015
Family_Pasteurellaceae               0.012752
Family_Bacillaceae                   0.012428
Route_Direct                         0.011787
Family_Bartonellaceae                0.011041
Family_Vibrionaceae                  0.010594
Family_Enterococcaceae               0.010384
Family_Anaplasmataceae               0.010380
Family_Mycobacteriaceae              0.009877
Family_Arcobacteraceae               0.009817
Family_Moraxellaceae                 0.009312
Family_Xanthomonadaceae              0.009030
Route_Direct                         0.008591
Family_Burkholderiaceae              0.007978
Family_Campylobacteraceae            0.007137
Family_Alcaligenaceae                0.005792
Family_Mycoplasmataceae              0.005666
Family_Neisseriaceae                 0.004331
Family_Nocardiaceae                  0.004078
Family_Streptococcaceae              0.003414
Family_Corynebacteriaceae            0.003301
Family_Fusobacteriaceae              0.003220
Family_Listeriaceae                  0.003134
Family_Coxiellaceae                  0.002960
Family_d                             0.002894
Family_Legionellaceae                0.002248
Family_Leptotrichiaceae              0.001405
Family_Helicobacteraceae             0.000000
dtype: float64
In [72]:
import seaborn as sns
f, ax = plt.subplots(figsize=(20, 20))
ax = sns.barplot(x=feature_scores, y=feature_scores.index, data=bact_new)
ax.set_title("Visualize feature scores of the features")
ax.set_yticklabels(feature_scores.index)
ax.set_xlabel("Feature importance score")
ax.set_ylabel("Features")
plt.show()
In [73]:
num=1
test_sample=X_test.iloc[num,:]
In [74]:
import lime
from lime import lime_tabular
explainer1 = lime_tabular.LimeTabularExplainer(
    training_data=np.array(X_train),
    feature_names=X_train.columns.values,
    class_names=['Nonsevere', 'Severe'],
    mode='classification',
    verbose=True,
    random_state=21)
exp1 = explainer1.explain_instance(
    data_row=test_sample, 
    predict_fn=RF1.predict_proba,num_features=20)

Intercept 1.1090296471834078
Prediction_local [0.40455556]
Right: 0.34875824175824177

C:\Users\KANMANIVISHWAA\anaconda3\lib\site-packages\sklearn\base.py:450: UserWarning: X does not have valid feature names, but RandomForestClassifier was fitted with feature names
  warnings.warn(
In [75]:
plt=exp1.as_pyplot_figure()
plt.tight_layout()
In [76]:
exp1.show_in_notebook(show_table=True, show_all=False)
In [77]:
import shap
explainer=shap.TreeExplainer(RF1)
shap_values=explainer.shap_values(X_test)
In [78]:
shap.initjs()
shap.force_plot(explainer.expected_value[1],shap_values[1][0,:],test_sample)
Out[78]:
Visualization omitted, Javascript library not loaded!
Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). If you are viewing this notebook on github the Javascript has been stripped for security. If you are using JupyterLab this error is because a JupyterLab extension has not yet been written.
In [79]:
shap.initjs()
shap.force_plot(explainer.expected_value[1],shap_values[1],X_test)
Out[79]:
Visualization omitted, Javascript library not loaded!
Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). If you are viewing this notebook on github the Javascript has been stripped for security. If you are using JupyterLab this error is because a JupyterLab extension has not yet been written.
In [80]:
shap.summary_plot(shap_values[1],X_test)
In [81]:
num>1
test_sample_2=X_test.iloc[num,:]
In [82]:
import lime
from lime import lime_tabular
explainer2 = lime_tabular.LimeTabularExplainer(
    training_data=np.array(X_train2),
    feature_names=X_train2.columns.values,
    class_names=['Leastsevere','Severe', 'Moresevere','Mostsevere'],
    mode='classification',
    verbose=True,
    random_state=21)
exp2 = explainer2.explain_instance(
    data_row=test_sample_2, 
    predict_fn=RF2.predict_proba,num_features=20,top_labels=4)

Intercept 0.6030929032937256
Prediction_local [0.04102163]
Right: 0.0
Intercept 0.9372817310515783
Prediction_local [0.13922757]
Right: 0.004
Intercept 0.1215473549308494
Prediction_local [0.54083382]
Right: 0.276
Intercept 0.5546150172295405
Prediction_local [0.34578499]
Right: 0.72

X does not have valid feature names, but RandomForestClassifier was fitted with feature names
In [83]:
plt=exp2.as_pyplot_figure()
In [84]:
exp2.show_in_notebook(show_table=True, show_all=False)
In [85]:
import shap
explainer_2=shap.KernelExplainer(RF2.predict_proba,X_train2)
Rf2_shap_values=explainer.shap_values(X_test2)

X does not have valid feature names, but RandomForestClassifier was fitted with feature names
Using 167 background data samples could cause slower run times. Consider using shap.sample(data, K) or shap.kmeans(data, K) to summarize the background as K samples.
In [86]:
shap.initjs()
shap.force_plot(explainer_2.expected_value[1],Rf2_shap_values[1][0,:],test_sample)
Out[86]:
Visualization omitted, Javascript library not loaded!
Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). If you are viewing this notebook on github the Javascript has been stripped for security. If you are using JupyterLab this error is because a JupyterLab extension has not yet been written.
In [87]:
shap.initjs()
shap.force_plot(explainer_2.expected_value[1],Rf2_shap_values[1],X_test)
Out[87]:
Visualization omitted, Javascript library not loaded!
Have you run `initjs()` in this notebook? If this notebook was from another user you must also trust this notebook (File -> Trust notebook). If you are viewing this notebook on github the Javascript has been stripped for security. If you are using JupyterLab this error is because a JupyterLab extension has not yet been written.